Pensoft blog - Part 78

Artificial neural networks could power up curation of natural history collections

Deep learning techniques manage to differentiate between similar plant families with up to 99 percent accuracy, Smithsonian researchers reveal

Millions, if not billions, of specimens reside in the world’s natural history collections, but most of these have not been carefully studied, or even looked at, in decades. While containing critical data for many scientific endeavors, most objects are quietly sitting in their own little cabinets of curiosity.

Thus, mass digitization of natural history collections has become a major goal at museums around the world. Having brought together numerous biologists, curators, volunteers and citizens scientists, such initiatives have already generated large datasets from these collections and provided unprecedented insight.

Now, a study, recently published in the open access Biodiversity Data Journal, suggests that the latest advances in both digitization and machine learning might together be able to assist museum curators in their efforts to care for and learn from this incredible global resource.

A team of researchers from the Smithsonian Department of Botany, Data Science Lab, and Digitization Program Office recently collaborated with NVIDIA to carry out a pilot project using deep learning approaches to dig into digitized herbarium specimens.

*Smithsonian researchers classifying digitized herbarium sheets.*

Their study is among the first to describe the use of deep learning methods to enhance our understanding of digitized collection samples. It is also the first to demonstrate that a deep convolutional neural network–a computing system modelled after the neuron activity in animal brains that can basically learn on its own–can effectively differentiate between similar plants with an amazing accuracy of nearly 100%.

In the paper, the scientists describe two different neural networks that they trained to perform tasks on the digitized portion (currently 1.2 million specimens) of the United States National Herbarium.

The team first trained a net to automatically recognize herbarium sheets that had been stained with mercury crystals, since mercury was commonly used by some early collectors to protect the plant collections from insect damage. The second net was trained to discriminate between two families of plants that share a strikingly similar superficial appearance.

*Sample herbarium specimen image of stained clubmoss.*

The trained neural nets performed with 90% and 96% accuracy respectively (or 94% and 99% if the most challenging specimens were discarded), confirming that deep learning is a useful and important technology for the future analysis of digitized museum collections.

“The results can be leveraged both to improve curation and unlock new avenues of research,” conclude the scientists.

“This research paper is a wonderful proof of concept. We now know that we can apply machine learning to digitized natural history specimens to solve curatorial and identification problems. The future will be using these tools combined with large shared data sets to test fundamental hypotheses about the evolution and distribution of plants and animals,” says Dr. Laurence J. Dorr, Chair of the Smithsonian Department of Botany.

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Original source:

Schuettpelz E, Frandsen P, Dikow R, Brown A, Orli S, Peters M, Metallo A, Funk V, Dorr L (2017) Applications of deep convolutional neural networks to digitized natural history collections. Biodiversity Data Journal 5: e21139. https://doi.org/10.3897/BDJ.5.e21139

When lemons give you life: Herpetofauna adaptation to citrus orchards in Belize

Natural habitat areas exhibit similar abundances and diversity of herpetofauna as citrus orchards and reclaimed orchard forests in Stann Creek, Belize, reports a comparative study by researchers Russell Gray and Dr. Colin Strine of Suranaree University of Technology (SUT), Thailand.

The scientists utilized several drift-fence arrays equipped with double-funnel traps to monitor and compare reptile and amphibian communities in a lowland broadleaf forest, a lime orchard and a reclaimed citrus orchard at the Toucan Ridge Ecology and Education Society (TREES) field station. Their study was recently published in the open-access journal ZooKeys.

Often referred to as Central America’s “hidden gem” for its abundance of undisturbed rainforests and natural beauty, Belize has a long-standing record for vigorously protecting and maintaining their forested areas. However, just as in any other developing country, its primary sector is expanding with agricultural land clearings becoming more frequent with newly established properties.

Approximately midway through the study (June – September 2016), the site was hit by Hurricane Earl, a Category 1 hurricane. The hurricane-force winds altered the canopy cover significantly over the forested study sites, due to felled trees and broken branches.

Surprisingly enough, the herpetofauna remained relatively unchanged in the aftermath of Earl. The phenomenon revealed that not only were herpetofaunal communities lacking sensitivity to anthropogenic changes in the area, but also to extreme weather events, even though these had affected most of the standing vegetation.

Some notable observations occurred within three days of Hurricane Earl, according to Russell Gray:

“One of the trapping system was catching arboreal [tree climbing] snake species, like the cat-eyed snake and blunt-headed tree snake. This wasn’t only interesting because arboreal snakes were caught in terrestrial traps, but rather because they were never caught in our traps during the study up to this point.”

“Even more interesting is that they were caught exclusively in the manicured orchard area, which makes me wonder if they somehow predicted falling trees and fled to the only habitat without them. Some animals appear to forecast weather events due to sudden or drastic changes in environmental conditions. I wonder if this is a similar case.”

Amongst other notable scientific discoveries reported during the project were two new accounts of the Petén Centipede Snake (Tantilla hendersoni), one of which was the first documented male of the species. This secretive snake had only been documented once prior to the study and is the only endemic snake species to Belize.

Further noteworthy instances were two range extensions for relatively data deficient species – one for the Doflein’s Salamander (Bolitoglossa dofleini) and another for the Ringneck Coffee Snake (Ninia diademata).

Besides providing important data on herpetofauna assemblages in various disturbed and undisturbed habitats in Belize, the research identifies future conservation methods to be considered.

The study serves as new evidence that as long as agricultural areas remain surrounded with natural habitat buffers, they have little effect on herpetofaunal communities.

Replicates of this study are encouraged by the authors and can be utilized as a feasible and efficient way to monitor reptiles and amphibians in Belize.

Although Belize still preserves a considerable amount of intact forest cover, there are several on-going conservation concerns. Besides agricultural land clearings, there are constant struggles with xate poachers, or “Xateros”, on the Guatemalan border, as well as illegal logging activities and illegal off-season hunting.

Unfortunately, reptiles and amphibians have been understudied in comparison to other vertebrates and government action is rarely enforced on their conservation throughout the Neotropics.

A striking example of this relates to the only critically endangered reptile in Belize – the Hickatee turtle (Dermatemys mawii). Although the species is likely to become extinct, it is still traditionally collected for its culinary value, while its hunting is banned only in May.

In conclusion, the authors note that it is crucial to pay close attention to anthropogenic activity and the potential repercussions it may have on native species. With extensive and active efforts to study Mesoamerican herpetofauna, proper conservation efforts can be implemented and focused.

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Original Source:

Gray R, Strine CT (2017) Herpetofaunal assemblages of a lowland broadleaf forest, an overgrown orchard forest and a lime orchard in Stann Creek, Belize. ZooKeys 707: 131-165. https://doi.org/10.3897/zookeys.707.14029

DNA study in the Pacific reveals 2000% increase in our knowledge of mollusc biodiversity

Lead author Dr Helena Wiklund examining specimens on the RV Melville in October 2013

Scientists working in the new frontier for deep-sea mining have revealed a remarkable 2000% increase in our knowledge of the biodiversity of seafloor molluscs.

The 21 mollusc species newly described thanks to the latest DNA-taxonomy methodology

Tweny-one species, where only one was previously known, are reported as a result of the research which applied the latest DNA-taxonomy methodology to mollusc specimens collected from the central Pacific Clarion Clipperton Zone (CCZ) in 2013. They are all described in the open access journal ZooKeys.

Among the discoveries is a monoplacophoran mollusc species regarded as a ‘living fossil’, since it is one the ancestors of all molluscs. This is the first DNA to be collected from this species and the first record of it from the CCZ mining exploration zone – a vast 5-million-km² region of the central Pacific that is regulated for seabed mining by the International Seabed Authority.

“Despite over 100 survey expeditions to the region over 40 years of mineral prospecting, there has been almost no taxonomy done on the molluscs from this area,” says lead author Dr Helena Wiklund of the The Natural History Museum in London (NHM).

Dr Wiklund undertook a comprehensive DNA-based study of the molluscs to confirm species identities and make data available for future taxonomic study. This was coupled with the expertise of the NHM’s Dr John Taylor, who led the morphological work.

The molluscs were found in samples taken on and in the mud surrounding the potato-sized polymetallic nodules that are present in high abundance across the CCZ. These nodules are the target for potential deep-sea mining being rich in cobalt, copper, nickel, manganese and other valuable minerals.

The data are vital for the future environmental regulation of deep-sea mining, but have also revealed surprising patterns.

“I was amazed to discover that specimens collected during the 19th century by HMS Challenger were probably the same as ours over a range of 7000 km, but that data lodged on genetic databases from closer but shallower depths is likely to be from a different species,” comments Dr Thomas Dahlgren, population geneticist at Uni Research, Norway and University of Gothenburg, Sweden, who studied in detail a species called Nucula profundorum.

“Our efforts are now focussing on studying the DNA from many more samples of this species to examine connectivity and potential resilience to deep-sea mining,” he added.

Dr Thomas Dahlgren sieving sediments to find new clam and snail species

“It is a simple truth that we cannot move forward on regulatory approval for deep-sea mining without fundamental baseline data on what animals actually live in these regions,” says Principal Investigator of the NHM Deep-sea Systematics and Ecology Research Group, Dr Adrian Glover.

“Our work has highlighted obvious gaps in our knowledge, but also shown that with even relatively modest effort, we can greatly increase our understanding of baseline biodiversity using DNA-taxonomy.”

Creating a library of archived DNA-sequenced samples from known species allows for the future possibility of using the latest environmental DNA (eDNA) methods to ‘search’ for these species using just tiny samples of mud or seawater.

“Its akin to forensic science’, says Dr Glover. “You can’t use eDNA to find the criminals or species unless you have a library of information to compare them too”.

All data and specimens from the study have been lodged at the NHM and online repositories to make them accessible for future study. Of particular importance are the frozen tissue collections, which are housed in the state-of-the-art Molecular Collections Facility at the NHM and available for loan or further DNA work.

Original source:

Wiklund H, Taylor JD, Dahlgren TG, Todt C, Ikebe C, Rabone M, Glover AG (2017) Abyssal fauna of the UK-1 polymetallic nodule exploration area, Clarion-Clipperton Zone, central Pacific Ocean: Mollusca. ZooKeys 707: 1–46. https://doi.org/10.3897/zookeys.707.13042

Two Caribbean bird-catcher trees named after two women with overlooked botanical work

Known for their biodiversity richness, the Caribbean Islands are now adding two new species of bird-catcher trees to their list of botanical treasures. Commonly referred to as bird-catcher trees, the species whose ripe fruits are sticky and can be glued to birds, are from the four-o’clock family (Nyctaginaceae) and only found in Puerto Rico.

Baptised Pisonia horneae and Pisonia roqueae by authors Marcos A. Caraballo-Ortiz, doctoral candidate at The Pennsylvania State University, US and Jorge C. Trejo-Torres, researcher at The Institute for Regional Conservation in Florida, US, the two unusual trees were named to honor the unrecognised work of two extraordinary self-driven women who devoted decades on educational projects in botany. The research was published in the open access journal Phytokeys.

“Finding large organisms new to science from a relatively small and well-studied island seems implausible, but this recent naming of the two large trees from Puerto Rico proves that explorations in nature and museums can still produce exciting novelties.” explains Trejo-Torres.

The two new trees belong to an extraordinary genus (Pisonia), containing rare plants mainly known for the ability to tangle birds with their sticky fruits, which inspired the common name “bird-catcher” used in the Pacific region. Characteristic for the two new trees are also swollen trunks that wrap over the rocks resembling an elephant foot with toes.

“Birds are the main dispersal agents for Pisonia trees, carrying the sticky fruits glued to their feathers to distant islands. However, sometimes these fruits can trap too tightly and even kills birds, as seen in documentaries.” remarks lead author, Caraballo-Ortiz. “So far, we do not know of cases where birds have been trapped by the sticky fruits of the new species, but future studies will explore this possibility”

One of the trees, Pisonia horneae, is dedicated to Frances W. Horne (1873-1967), an American illustrator who spent 45 years painting 750 watercolors of plants from Puerto Rico, of which only a small fraction were published. The other tree, Pisonia roqueae, was named after Dr. Ana Roqué de Duprey (1853-1933), a Puerto Rican educator, writer, and suffragist. As an amateur ethnobotanist, she spent over three decades to prepare a manuscript aimed to make botany accessible to the general public, which was never published.

“It only seemed natural to name the two new species after these two extraordinary women who spent decades on large educational projects aimed to divulge botanical knowledge in Puerto Rico.” explains Trejo-Torres. “Just like the two large trees remained unrecognised by science until now, the enormous efforts of these two women, who dedicated part of their lives to botanical work, remained largely unrecognised by the community.”

“The scientific relevance of naming these trees is that they thrive in the Puerto Rican forests, including the Luquillo Mountains, which are among the most well studied areas in the world. World-scattered ecologists and conservationists actively working on Puerto Rican forests and plants now have a nice and surprising update to make in their databases.” concluded Caraballo-Ortiz.

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Original source:

Caraballo-Ortiz MA, Trejo-Torres JC (2017) Two new endemic tree species from Puerto Rico: Pisonia horneae and Pisonia roqueae (Nyctaginaceae). PhytoKeys 86: 97-115. https://doi.org/10.3897/phytokeys.86.11249

Additional Information:

Funding organisations include the United States Department of Agriculture-Forest Service-International Institute of Tropical Forestry, The Institute for Regional Conservation, and The Alfred P. Sloan Foundation.

New open-access journal Metabarcoding & Metagenomics joins the lines of publisher Pensoft

The new innovative academic journal makes use of the one-of-a-kind publishing platform ARPHA and its collaborative writing tool via the ARPHA-XML workflow

A new innovative open-access academic journal Metabarcoding and Metagenomics (MBMG) is launched to welcome novel papers from both basic and applied aspects.

Focusing on genetic approaches to study biodiversity across all ecosystems, MBMG covers a considerably large scope of research including environmental, microbial and applied metabarcoding and metagenomics (especially DNA-based bioassessment and -monitoring, quarantine, nature conservation, species invasions, eDNA surveillance), as well as associated topics, such as molecular ecology, DNA-based species delimitation and identification, and other emerging related fields. Submissions of bioinformatic approaches to MBMG (algorithms, software) are also encouraged.

Featuring novel article formats and data publishing workflows, MBMG is to reflect the rapid growth in the use of metabarcoding and metagenomics in life and environmental sciences.

Issued via ARPHA – the first ever publishing platform to support manuscripts all the way from authoring to peer review to publication and dissemination, designed by the academic publisher and technology provider Pensoft, the new journal is to host a wide range of outcomes from across the research cycle, including data, models, methods, workflows, software, perspectives, opinions, implementation strategies, as well as conventional research articles.

While the above-mentioned publication types are already available in other journals published on the ARPHA platform, such as Research Ideas and Outcomes (RIO), Biodiversity Data Journal and One Ecosystem, MBMG provides five extra domain-specific article types, namely: Emerging Technique, Applied Study, DNA Barcode Release, Primer Validation and Probe Validation.

The journal’s articles are to be available in three formats (PDF, XML, HTML) and full of semantic enhancements for better human- and machine-readability and discoverability. The XML-based workflow also ensures that content and data are available for extraction, indexing and re-use immediately after publication.

With Pensoft standing for transparent, reproducible and open science, the authors at MBMG are strongly encouraged to make all data publicly available either within the publication itself, or to link to external repositories. In their turn, the peer reviewers are also suggested to provide public access to their reviews and identities.

In time for the launch, MBMG has already gathered a team of experienced and renowned scientists from across the globe together on its editorial and advisory board.

“I am pleased to introduce the Metabarcoding and Metagenomics journal to the family of Pensoft,” says Prof. Lyubomir Penev, Founder and Managing Director at Pensoft. “With its exhaustive scope and advanced services and concept, I believe it fills fantastically a niche in our strong portfolio of mostly biodiversity- and ecology-themed journals.”

“Metabarcoding and metagenomics approaches are rapidly progressing and revolutionise research and its application alike,” Chief Editor Prof. Florian Leese states. “With the MBMG journal we provide an ideal platform to respond to this rapidly growing field, nucleate the emerging knowledge and stimulate further development.”

The first batch of research papers published in MBMG are now available on their new website.

“MBMG not only complements the range of journals in the field of molecular environmental life sciences, but also stands out as a novel outlet providing several unique features designed to help researchers to prepare for, and professionally deal with, the massive “deluge” of data,” reads the Editorial.

To celebrate the launch, MBMG starts with a tempting offer to potential authors: publishing will be completely free of charge during the beginning stages of the journal.

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Follow Metabarcoding and Metagenomics on Twitter | Facebook.

Heat-loving Australian ants believe in diversity, hint 74 species new to science

The ‘furnace ants’ or ‘honeypot ants’ present a very large genus of ants, Melophorus, confined to Australia. Long believed to be megadiverse, some scientists have even suggested that the group may contain ‘well over 1000 species’. However, to this point, only 32 species and subspecies had been described.

Scientists Dr Brian Heterick of Curtin University, Dr Mark Castalanelli of Ecodiagnostics Pty Ltd and Dr Steve Shattuck of the Australian National University, funded by an internationally competitive Australian Biological Resources (ABRS) grant, set out to find the true facts.

As a result, they discovered as many as 74 new species belonging to Melophorus. In their study, published in the open access journal ZooKeys, they also provide a taxonomic key to the workers of a total of 93 species in the genus.

Among the studied ants, there are quite bizarre ones, including a species (Melophorus hirsutus) whose eyes are strangely protruding out of his head to a varying degree. In the extreme cases, the eyes are so pointy that could be likened to ice-cream cones. Named many years ago, this ant appears to be older than the rest of the examined living species. Furthermore, unlike most of them, it does not seem adapted to heat. It is confined to the wet eastern coast of Australia.

Dr Heterick spent two weeks collecting specimens in the often rugged and forbidding terrain of Western Australia, while the team also asked a number of major museum collections to loan them specimens.

The newly collected ants were placed in alcohol and subjected to genetic tests using one mitochondrial and four nuclear genes. The findings were then compared with those from physical examinations to prepare the taxonomic key – a set of distinctive features per species that can be used to differentiate within the group.

Given the generally complex nature of these ants, the authors expect for the genus to further expand in future. They speculate that even though the numbers may increase to around 100 species, not the ‘well over 1000’ previously predicted, they still illustrate an incredible diversity.

The authors estimate that Melophorus arose around 35 million years ago. The closest relatives of the genus are also confined to the Australasian region with the exception of a single genus living in South America.

Furthermore, the genus is also quite astonishing thanks to another trait shared among the species.

“By the way, this group of ants has a thing or two to tell those of us who get lost easily!” comments lead author Dr Brian Heterick.

“They can find their way home in a featureless landscape by means of an internal compass influenced by information gathered on earlier journeys. We are not the first species to use a computing system!”

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Original source:

Heterick B, Castalanelli M, Shattuck S (2017) Revision of the ant genus Melophorus (Hymenoptera, Formicidae). ZooKeys 700: 1-420. https://doi.org/10.3897/zookeys.700.11784

An extraordinary cave animal found in Eastern Turkmenistan

A remote cave in Eastern Turkmenistan was found to shelter a marvelous cave-adapted inhabitant that turned out to represent a species and genus new to science. This new troglodyte is the first of its order from Central Asia and the first strictly subterranean terrestrial creature recorded in the country.

Kaptarhana cave is located at the foot of Koytendag Mountain, one of the most distinctive mountain landscapes in Central Asia. A curious amalgam of desert landscapes, often highly dissected by ravines, foothills with ridges, cuestas and fan plains, the mountain is a potential home to key biodiversity gems still awaiting discovery.

Also remarkable for its richness of caves and other limestone formations, Koytendag Mountain has more than 300 caves, sinkholes and potholes, hitherto registered from its territory, including the sixth largest cave system in Asia Gap Goutan/Promezdutachnaya stretched at more than 57 km underground. Also worthy of a mention is the beautiful cave Gulshirin, known for its snow white passages and extraordinary formations.

Another fine example, cave Kaptarhana, presents a unique habitat for a high number of cave-adapted animals, among which is the new species of a few millimetres long, pale and eyeless insect-like creature, whose relatives in the order Diplura also go by the name of two-pronged bristletails.

The scientists named it Turkmenocampa mirabilis, where the genus name (Turkmenocampa) refers to the creature’s country of origin (Turkmenistan), while the species name (mirabilis) means “unusual, amazing, wonderful, remarkable” in Latin to highlight its unique morphology and position among its relatives.

The new species is described in the open access journal Subterranean Biology by Dr. Alberto Sendra, University of Alcalá, Spain, Prof. Boris Sket, University of Ljubljana, and Prof. Pavel Stoev, National Museum of Natural History, Bulgaria.

In fact, Stoev and Sket were the first speleobiologists to visit and explore Kaptarhana in nearly 43 years. The survey was part of their study into the caves of Koytendag State Nature Reserve, Turkmenistan, conducted in 2015 and endorsed by a Memorandum of Understanding between the State Committee on Environment Protection and Land Resources of Turkmenistan and the Royal Society for the Protection of Birds.

To discover the new species, the scientists spent about 8 hours in the cave looking for specimens and placed pitfall traps with smelly cheese used as a bait. While visual observations had no success due to the cave being very spacious, a number of exemplars of the hitherto undescribed animal fell victims of the traps.

“What we have here is not only a new remarkable organism, but also an amazing and unusual cave critter that has undergone a long evolutionary journey to adapt to the underground environment of Central Asia,” says the lead author Alberto Sendra.

The authors see their latest discovery as a proof of the importance of Kaptarhana as a refuge for a number of endemic invertebrates and an opportunity to draw attention to its protection under the laws of Turkmenistan.

“While many speleobiologists consider the terrestrial cave fauna in Central Asia as poor, it is places such as Kaptarhana that can turn the tables by giving us new insights about the biodiversity richness, evolutionary history, formation and functioning of the underground ecosystems of this part of the world.” comments Stoev.

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Original source:

Sendra A, Boris Sket B, Stoev P (2017) A striking new genus and species of troglobitic Campodeidae (Diplura) from Central Asia. Subterranean Biology 23: 47-68. https://doi.org/10.3897/subtbiol.23.14631

Connecting plants and society: The Shenzhen Declaration, a new roadmap for plant sciences

Environmental degradation, unsustainable resource use, and biodiversity loss are just a few points in the long list of pertinent issues that call for collaborative solutions from science and society together.

Unanimously supported by participants at the XIX International Botanical Congress, held in July 2017, Shenzhen, China, the Shenzhen Declaration for Plant Sciences, runs under the slogan of “Uniting plant sciences and society to build a green, sustainable Earth” and comes in response to the rapid changes experienced by both our Planet and society.

On 29 July 2017 in the closing session of the Congress, nearly 7,000 plant scientists from 77 countries endorsed a statement to focus their research and educational efforts on finding solutions to the growing problems of of our changing world.

Central to the declaration comes a commitment from its signatories and supporters alike to take immediate in both their lifestyles and their research programs to find solutions before an environmental threshold is crossed that will inevitably lead to irreversible degradation of our societies, natural habitats, and biodiversity.

Although it was largely agreed that the immense changes are the result of unbridled human activities, it was also made clear that it is still in society’s power to find solutions to reverse or slow down some of these processes.

Many scientists believe that humanity and the planet may have already crossed that threshold,” explain PhytoKeys Editor-in-Chief, John Kress, Smithsonian Institution, USA and his Deputy Editor-in-Chief Sandy Knapp, Natural History Museum London, UK, in their dedicated Editorial for the journal. “However, the authors of the Declaration and the botanists who have endorsed it believe that time still exists for answers to be found and implemented. However, that time is short.”

The Declaration calls for collaborative approaches by the rapidly evolving field of Plant Science and other disciplines and society, including implementation of new technologies, valuing local and traditional knowledge and greater engagement with the public.

Paving a solid and inspiring roadmap for development for the botanical community, the Declaration outlines seven priorities:

To become responsible scientists and research communities who pursue plant sciences in the context of a changing world.
To enhance support for the plant sciences to achieve global sustainability.
To cooperate and integrate across nations and regions and to work together across disciplines and cultures to address common goals.
To build and use new technologies and big data platforms to increase exploration and understanding of nature.
To accelerate the inventory of life on Earth for the wise use of nature and the benefit of humankind.
To value, document, and protect indigenous, traditional, and local knowledge about plants and nature.
To engage the power of the public with the power of plants through greater participation and outreach, innovative education, and citizen science.

Find the full text of the Shenzhen Declaration, co-published in the open access journal PhytoKeys and the Journal of Systematics and Evolution.

“We believe that, by working together, we can achieve these goals and connect the increasingly innovative plant sciences with the needs and strengths of human societies.” comment the authors of the Declaration. “We strongly believe that only through such collaboration we can work towards creating new paths to a green, sustainable future for Earth, where plants and people in harmony is at the centre.”

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Original Sources:

Shenzhen Declaration Drafting Committee (2017) The Shenzhen Declaration on Plant Sciences – Uniting plant sciences and society to build a green, sustainable Earth. PhytoKeys 86: 3-7. https://doi.org/10.3897/phytokeys.86.20859

Kress WJ, Knapp S (2017) The Shenzhen Declaration on Plant Sciences: Too late or just in time? PhytoKeys 86: 1-2. https://doi.org/10.3897/phytokeys.86.20712

* Image Credits: This image is designed for the Shenzhen Declaration on Plant Sciences by Genlin Jiao, Alice Tangerini and Jun Wen. Photo credits go to Chip Clark, Genlin Jiao, Hong Jin, Sandra Knapp, Steven Manchester, Jun Wen, Bob Wick and Li Zhang. The picture on the top row (right) appeared in the Los Angeles Times on April 7, 2017.

Six new sponge species and new symbiotic associations from the Indonesian coral triangle

Comprising more than 17,000 islands, the Indonesian archipelago is one of the world’s most biodiverse places on Earth.

Sponges, aquatic organisms whose bodies consist of numerous pores to allow the ingress of water, are key components of this richness and play a fundamental role in the survival of coral reef habitats. Furthermore, they are also known for their medicinal benefits.

Unfortunately, due to the paucity of taxonomic expertise, the sponges from the Indonesian reefs are often ignored in monitoring surveys and conservation programmes, while their diversity is largely underestimated.

Researchers from the Italian Università Politecnica delle Marche and Università degli Studi di Genova, PharmaMar, Spain, and University of Sam Ratulangi, Indonesia, describe six new species in their paper in the open access journal, ZooKeys.

Inspired by their extraordinary biodiversity, the researchers teamed up with the pharmaceutical company PharmaMar to conduct several expeditions in the waters of North Sulawesi Island.

The authors reported a total of 94 demosponge species belonging to 33 families living in the North Sulawesi Island. Amongst them, there are six species new to science and two previously unknown symbiotic relationships.

Seven of the recorded species were collected for the very first time since their original description.

However, these findings are still scarce, given the abundance of the sponges in similar localities in the Indonesian archipelago.

In conclusion, the authors note that the marine diversity in Indonesia is still far from being well known.

“Thanks to this impressive diversity, these areas are important spots for diving tourism and require the urgent development of sustainable tourism practices,” they say.

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Original source:

Calcinai B, Bastari A, Bavestrello G, Bertolino M, Horcajadas SB, Pansini M, Makapedua DM, Cerrano C (2017) Demosponge diversity from North Sulawesi, with the description of six new species. ZooKeys 680: 105-150. https://doi.org/10.3897/zookeys.680.12135

Light at the end of the tunnel: Restored forest now shelters dozens of endangered species

During the last twenty years, scientists worked hard to protect and restore the scattered patches of a dilapidated forest and its surroundings of agricultural and fallow vegetation in southern Benin.

With the help of their locally recruited assistants, Peter Neuenschwander, International Institute of Tropical Agriculture, Benin, and Aristide Adomou, University of Abomey-Calavi, Benin, successfully thinned out the alien timber growing there and introduced 253 species, whose seeds and plantlets they had managed to collect from the last remnants of the original forest. Their research article is published in the open access journal Nature Conservation.

Today, the rehabilitated forest in Drabo harbours about 600 species of plants and constitutes a sanctuary for many animals, including the critically endangered and endemic red-bellied monkey.

Over the course of the last two decades, pantropical weedy species declined, while West-African forest species increased in numbers. Of the former, fifty-two species, mostly trees, shrubs and lianas, are listed as threatened – more than those in any other existing forest in Benin. Furthermore, some of the critically endangered species amongst them can be found exclusively in the last small, often sacred forests in Benin, which while covering merely 0.02% of the national territory, harbour 64% of all critically endangered plant species.

“The biodiversity richness of the rehabilitated forests of Drabo now rivals that of natural rainforest remnants of the region,” note the authors.

The newly restored forest in Drabo is relatively easy to access due to its proximity to large towns. It is intended to become an educational and research centre maintained by the International Institute of Tropical Agriculture. In fact, it already serves as an exemplary forest in the region.

With their initiative, the scientists and their followers demonstrate that by involving local communities and taking their customs into consideration, the safety of exposed precious ecosystems, even if located in a densely populated area, can be effectively assured.

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Original source:

Neuenschwander P, Adomou AC (2017) Reconstituting a rainforest patch in southern Benin for the protection of threatened plants. Nature Conservation 21: 57-82. https://doi.org/10.3897/natureconservation.21.13906