Tag: botany

Italian Society of Vegetation Science signs with Pensoft to publish its journal on ARPHA

The first 2020 papers of the open-access, peer-reviewed international journal Plant Sociology are now available on the journal’s new, user-friendly and visually appealing website

Having succeeded the historical journals of the Italian Society of Vegetation Science (Società Italiana di Scienza della Vegetazione): Fitosociologia (1990-2011) and Notiziario della Societa Italiana di Fitosociologia (1964-1989), the open-access, peer-reviewed international journal Plant Sociology undergoes another major transformation by moving to the technologically advanced ARPHA Platform, after signing with the scholarly publisher and technology provider Pensoft.

As a result of the recently started partnership, the first 2020 papers of Plant Sociology are now available on the journal’s new website. All pre-2020 issues remain available on the former website.

With a wide scope covering vegetation studies from plant community to landscape level, Plant Sociology puts a special focus on topics such as Plant Sociology and vegetation survey for developing ecological models, as well as plant classification, monitoring, assessment, management and conservation, as long as the studies are based on rigorous and quantitative measures of physical and biological components.

Amongst the first newly published papers is an article by a team from the University of L’Aquila, which reports on two years of observations of the vegetation dynamics at the Gran Sasso – Monti della Laga National Park in central Italy, after the protected area suffered from an accidental fire of anthropogenic origin in 2017. With their study, the researchers aim to determine the potential of the Sentinel-2 satellite as a tool to measure, identify and monitor the short-term response of vegetation in a peculiar mountainous landscape.

Another new publication presents a phytosociological survey on the weed vegetation of two crops of Protected Designation of Origin: the bean “Fagiolo Cannellino di Atina” and the red pepper “Peperone di Pontecorvo” – both growing exclusively within a few hundreds of square kilometres in the Province of Frosinone (central Italy), conducted at four selected farms by researchers at the Sapienza University of Rome.

Thanks to the Pensoft’s signature open-access scholarly publishing platform ARPHA, Plant Sociology demonstrates a complete makeover, including a modern and user-friendly interface in addition to a long list of high-tech perks, meant to ensure that published articles are easy to discover, access, cite and reuse by both humans and machines all over the world.

Furthermore, all users of the journal’s system: authors, editors and reviewers alike, are to greatly benefit from ARPHA’s integrated approach to the publication process. This means that once submitted each manuscript goes through the whole cycle: from review and copy/layout editing to publication, dissemination and archiving without leaving ARPHA’s collaboration-focused online environment.

Plant Sociology has a completely renewed Editorial board, which sees Daniela Gigante from the University of Perugia in the role of Editor-in-Chief, and Simonetta Bagella (University of Sassari), Gianni Bacchetta (University of Cagliari) and Daniele Viciani (University of Florence) as Co-editors. The Editorial board is complemented by a Consultant editor and an Editorial secretary (respectively, Edoardo Biondi and Diana Galdenzi, both from the Polytechnic University of Marche, Ancona). A large, international Editorial team includes 35 members with specific skills and long-dated expertise in various fields related to vegetation science. A dedicated Social media team takes care of the dissemination of the journal.

“At the Plant Sociology‘s Editorial board, we are looking with great expectations to the cooperation with Pensoft, certain that the publisher’s skills and experience will support the journal in its growth and consolidation as an international reference point for vegetation science studies,”
says Editor-in-Chief Dr Daniela Gigante.

“It’s delightful to have the Italian Society of Vegetation Science putting their trust in us with their signature journal. With our strong background in scholarly publishing, technology development and open science practices, I am certain that we are to provide the right venue for a high-quality and enterprising journal like Plant Sociology,”
says ARPHA’s and Pensoft’s founder and CEO Prof. Lyubomir Penev.

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“Oldest bamboo” fossil from Eocene Patagonia turns out to be a conifer

A recent examination revealed that Chusquea oxyphylla, a fossilised leafy branch from the early Eocene in Patagonia, which has been widely cited as the oldest bamboo fossil and as evidence for a Gondwanan origin of bamboos is actually a conifer. The results of the finding are published in the open-access journal Phytokeys.

A fossilised leafy branch from the early Eocene in Patagonia described in 1941 is still often cited as the oldest bamboo fossil and the main fossil evidence for a Gondwanan origin of bamboos. However, a recent examination by Dr. Peter Wilf from Pennsylvania State University revealed the real nature of Chusquea oxyphylla. The recent findings, published in the paper in the open-access journal Phytokeys, show that it is actually a conifer.

The corrected identification is significant because the fossil in question was the only bamboo macrofossil still considered from the ancient southern supercontinent of Gondwana. The oldest microfossil evidence for bamboo in the Northern Hemisphere belongs to the Middle Eocene, while other South American fossils are not older than Pliocene.

Over the last decades, some authors have doubted whether the Patagonian fossil was really a bamboo or even a grass species at all. But despite its general significance, modern-day re-examinations of the original specimen were never published. Most scientists referring to it had a chance to study only a photograph found in the original publication from 1941 by the famous Argentine botanists Joaquín Frenguelli and Lorenzo Parodi.

In his recent study of the holotype specimen at Museo de La Plata, Argentina, Dr. Peter Wilf revealed that the fossil does not resemble members of the Chusquea genus or any other bamboo.

“There is no evidence of bamboo-type nodes, sheaths or ligules. Areas that may resemble any bamboo features consist only of the broken departure points of leaf bases diverging from the twig. The decurrent, extensively clasping leaves are quite unlike the characteristically pseudopetiolate leaves of bamboos, and the heterofacially twisted free-leaf bases do not occur in any bamboo or grass,” wrote Dr. Wilf.

Instead, Wilf linked the holotype to the recently described fossils of the conifer genus Retrophyllum from the same fossil site, the prolific Laguna del Hunco fossil lake-beds in Chubut Province, Argentina. It matches precisely the distichous fossil foliage form of Retrophyllum spiralifolium, which was described based on a large set of data – a suite of 82 specimens collected from both Laguna del Hunco and the early middle Eocene Río Pichileufú site in Río Negro Province.

Retrophyllum is a genus of six living species of rainforest conifers. Its habitat lies in both the Neotropics and the tropical West Pacific.

The gathered evidence firmly confirms that Chusquea oxyphylla has nothing in common with bamboos. Thus, it requires renaming. Preserving the priority of the older name, Wilf combined Chusquea oxyphylla and Retrophyllum spiralifolium into Retrophyllum oxyphyllum.

The exclusion of a living New World bamboo genus from the overall floral list for Eocene Patagonia weakens the New World biogeographic signal of the late-Gondwanan vegetation of South America, which already showed much stronger links to living floras of the tropical West Pacific.

“The strongest New World signal remaining in Eocene Patagonia based on well-described macrofossils comes from fossil fruits of Physalis (a genus of flowering plants including tomatillos and ground cherries), which is an entirely American genus,” concludes Dr. Wilf.

Original source:
Wilf P (2020) Eocene “Chusquea” fossil from Patagonia is a conifer, not a bamboo. PhytoKeys 139: 77-89.
https://doi.org/10.3897/phytokeys.139.48717

Plant diversity and endemism in China: unreachable locations and diverse microclimates

The newly described Bulbophyllum reflexipetalum

A new issue of the scholarly, open-access and peer-reviewed journal PhytoKeys focuses on the Chinese biodiversity hotspots and their substantial role in understanding the country’s unique flora. The special issue embarks on a treasure hunt into China’s biodiversity hotspots, including the descriptions of 23 species previously unknown to science and new insights into the ecological diversity of ferns based on their DNA sequences.

In China, biodiversity-rich landscapes vary from the dry Northwest region, through the surrounded by massive mountain ranges of the Qinghai-Tibet Plateau, to the tropical and subtropical southern China. The combination of remote and hard to reach mountain areas and diverse microclimates promises high levels of endemism.

“With extended collaboration among Chinese scientists and coordination of networks on plant conservation and taxonomy across China, we synthesize a special issue entitled “Revealing the plant diversity in China’s biodiversity hotspots”, to present the latest findings by Chinese botanists, and to update knowledge of the flora for China and adjacent countries”, explained De-Zhu Li, professor of botany at Kunming Institute of Botany (KIB), Chinese Academy of Sciences (CAS), in the editorial.

Among the newly described species, four new members of the African violet family were found from a subtropical forest in Yunnan province in southern China, discovered by researchers from Xishuangbanna Tropical Botanical Garden, CAS and their collaborators. Half of them were found only from a sole population and require further botanical examinations to deploy the conservation priorities, remark the scientists.

In another paper, scientists Yun-Feng Huang and Li-Na Dong and Wei-Bin Xu, representatives of Guangxi Institute of Botany, revealed the discovery of a new species from the primrose family. Found nowhere outside the limestone areas in Liucheng county (Guangxi, China), this rare plant species is currently facing serious threats of extinction because of the fragility and sensitivity of its habitat to the environmental changes associated with the rapid economic development of China.

The newly described *Lysimachia fanii*
Credit: Yun-Feng Huang, Li-Na Dong, Wei-Bin Xu
License: CC-BY 4.0

Another team from the Guizhou University of Traditional Chinese Medicine and KIB describes a new representative of the parachute flowers. Ceropegia jinshaensis, characterized by the shape and size of its leaves and flowers.

“More conservation efforts are needed in this region to counteract the increasing anthropogenic disturbance and destruction”, state the leading authors from KIB, who discovered a new species of orchid in the Eastern Himalaya biodiversity hotspot.

The special issue features the description of additional two orchid species, discovered in Motuo, located at the Himalayan border between China, Myanmar and India. The region is well known for its vertical vegetation system, varying from tropical forest to permanent glaciers. Ji-Dong Ya and Cheng Liu from the KIB and Xiao-Hua Jin from the Institute of Botany, CAS underline that the difficult access to the area allows the thriving and diversification of plants.

Find the complete “Revealing the plant diversity in China’s biodiversity hotspots” special issue openly published in PhytoKeys at: https://phytokeys.pensoft.net/issue/1703/

Scientists challenge notion of binary sexuality with naming of new plant species

A collaborative team of scientists from the US and Australia has named a new plant species from the remote Outback. Bucknell University biology postdoctoral fellow Angela McDonnell and professor Chris Martine led the description of the plant that had confounded field biologists for decades because of the unusual fluidity of its flower form. The discovery, published in the open access journal PhytoKeys, offers a powerful example of the diversity of sexual forms found among plants.

The new species of bush tomato discovered in remote Australia provides a compelling example of the fact that sexuality among Earth’s living creatures is far more diverse – and interesting – than many people likely realize.

Bucknell University postdoctoral fellow Angela McDonnell and biology professor Chris Martine led the study following an expedition last year to relocate populations of the new plant, which were first noted by Australian botanists during the 1970s.

Herbarium specimens from those few earlier collections are peppered with notes regarding the challenge of identifying the sexual condition of this plant, which appeared at various times to be female, male, or bisexual.

According to Martine, about 85% of the planet’s quarter-million flowering plant species have flowers that are bisexual – with both male and female organs present in every blossom.

“So that’s already quite different than what some people might expect; but the remaining 15% or so come in all sorts of forms that push the envelope further, including unisexual flowers and (like we see in a plant like Cannabis) whole plants that are either male or female.”

“For the most part, a given plant species will stick to one primary and predictable type of sexual expression,” said Martine “but what makes Solanum plastisexum stand out is that it is one of a just a few plants that kind of do it all. It really seems like you never know what you’ll get when you come across it.”

When DNA studies in Martine’s lab offered proof that these plants were not only all the same thing, but a species not yet described, he, McDonnell, Jason Cantley (San Francisco State University), and Peter Jobson (Northern Territory Herbarium in Alice Springs) set out to hunt for populations along the unpaved Buchanan Highway in the remote northwestern region of the Northern Territory.

The botanists were able to collect numerous new specimens and have now published the new species description in the open-access journal PhytoKeys, choosing the name Solanum plastisexum as a nod to the notable variation exhibited by this plant in its sexual condition.

“This name, for us, is not just a reflection of the diversity of sexual forms seen in this species,” wrote the authors in the article. “It is also a recognition that this plant is a model for the sort of sexual fluidity that is present across the Plant Kingdom – where just about any sort of reproductive form one can imagine (within the constraints of plant development) is present.”

Also known as the Dungowan bush tomato, Solanum plastisexum is a distant cousin of the cultivated eggplant and is a close relative of two other Australian species recently discovered by Martine and colleagues that were also published in PhytoKeys: Solanum watneyi, named for Mark Watney, the space botanist of the book/film The Martian; and Solanum jobsonii, a species named last year for S. plastisexum co-author Jobson.

*S. plastisexum* with scientist Jason Cantley

The scientists hope that the naming of this latest new species turns a spotlight on the fact that nature is full of examples for the myriad ways in which living things behave sexually.

“In a way, S. plastisexum is not just a model for the diversity of sexual/reproductive form seen among plants – it is also evidence that attempts to recognize a “normative” sexual condition among the planet’s living creatures is problematic.”

“When considering the scope of life on Earth,” the authors conclude, “The notion of a constant sexual binary consisting of two distinct and disconnected forms is, fundamentally, a fallacy.”

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Bucknell sophomore Heather Wetreich, who measured and analyzed the physical characters of the new species using plants grown from seed in a campus greenhouse, joins McDonnell, Cantley, Jobson, and Martine as a co-author on the publication.

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Original source:

Citation: McDonnell AJ, Wetreich HB, Cantley JT, Jobson P, Martine CT (2019) Solanum plastisexum, an enigmatic new bush tomato from the Australian Monsoon Tropics exhibiting breeding system fluidity. PhytoKeys 124: 39-55. https://doi.org/10.3897/phytokeys.124.33526

New perennial brome-grass from the Iberian Peninsula named after Picos de Europa National Park

Picos de Europa National Park has given its name to a new species of perennial bromegrass, discovered in Spain. Bromus picoeuropeanus belongs to a rather underrepresented on the Iberian Peninsula perennial group within the grass genus Bromus, with the new species being just the fourth of all recognised wild species living in the Iberian territory.

Having worked on the systematics of Bromus for a long time, scientists Dr Carmen Acedo and Dr Félix Llamas, members of the Taxonomy and Biodiversity Conservation research group TaCobi of the Spanish University of León, were surprised to collect what seemed a so-far-unrecognised species of the rare for Iberia perennial group. The unlikely discovery of the new species was described and published in the open access journal PhytoKeys, while its type specimen is preserved on Herbarium LEB.

This is the preferred habitat of *Bromus picoeuropeanus* in stony and unstable soils, c. 1900 m elevation.

Failing to understand how it was possible that the new species has never been found in the over-studied territory of Picos de Europa National Park, the two researchers traveled back to the classic locality to confirm its presence and study the habitat. Interestingly, while the new species is located in a typical for the National Park habitat, only a single perennial Bromus species was previously known from the area.

Eventually, having spent more time studying and collecting samples of different taxa in the Park, the authors discovered several more individuals of the new species dwelling in stony areas at an altitude of 1600 – 2200m. While herbarium collections from the National Park revealed that samples were also collected some years ago by another botanist, the scarcity of populations of the new species is still striking given the abundance of other brome-grass species.

Unlike its sister species, the Picoeuropean brome-grass is a small rhizomatous herb up to 70 cm high. Another easy-to-recognize difference is its well-developed subterraneous vegetative organ, forming a long rootstalk called rhizome, which is an easy distinctive trait.

“Given the inaccessibility of the areas, the mountainous topography and the few grass-species-loving botanists, this species was ignored until now. Probably the genus Bromus has undergone some local speciation on this isolated place, but exactly how this occurred requires further investigation,” explain the authors noting the isolation of the new species from its relatives in the area.

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Original Source:

Acedo C, Llamas F (2019) A new species of perennial Bromus (Bromeae, Poaceae) from the Iberian Peninsula. PhytoKeys 121: 1-12. https://doi.org/10.3897/phytokeys.121.32588

Described 28 years post-collection, new grass species makes a strong case for conservation

Originally collected 28 years ago in Ecuador, new species Poa laegaardiana has been just described, only to find out its prospects for surviving in its type location seem bleak nowadays. The study was published in the open access journal PhytoKeys.

When roaming in the Cordillera de los Andes of Ecuador, near the village of Facundo Vela, little did Smithsonian scientist and author, Dr. Paul M. Peterson, know that a small grass specimen will not only turn out to be an intriguing new species, but will also make a big statement on the importance of conservation.

Scientific drawing showing what makes new species P. laegaardiana distinct from its congeners

Almost three decades after its original collection the new species P. laegaardiana has finally emerged from its herbarium collection, but the story took an unexpected twist.

It took the authors a single Google Earth search to find out that what used to be the natural habitat of the newly found densely tufted bunchgrass, is now occupied predominantly by small farms.

Heavy agricultural use of the terrain, poses a good possibility for P. laegaardiana to have already been extirpated from this location. With the species currently known only from this area, chances are that this newly described species, might in fact turn out to be already extinct.

“Further studies are needed to search the area and browse collections for specimens from different locations,” explains Dr. Peterson. “But, in fact, it may well be that with our study we are documenting a possible extinction of a species, happening in the space of just 30 years. The story of P. laegaardiana serves to show how human-induced habitat loss can indeed be a major threat to the survival of life on Earth.”

The new species was named after renowned Danish botanist Simon Laegaard, who has made extensive collections in South America, Greenland, Ecuador, and Bolivia (accompanied by the authors) contributing to the documentation of the flora to make informed conservation and management plans.

Google Earth image comparison between the area of collection in 2011 and today. With the area having been plowed, chances of the grass still existing there are small, however it may still be found along the margins of the fields. CREDIT Left: @2018DigitalGlobe; Right: @2018Google @2018CNES/Airbus

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Original Source:

Peterson PM, Soreng RJ (2018) Poa laegaardiana, a new species from Ecuador (Poaceae, Pooideae, Poeae, Poinae). PhytoKeys 100: 141-147. https://doi.org/10.3897/phytokeys.100.25387

First-ever fern checklist for Togo to help decision makers in the face of threats to biodiversity

Maidenhair fern (*Adiantum schweinfurthii*) occurring in dense forests.

Ferns and their allied species, which together comprise the pteridophytes, are vascular non-flowering plants that reproduce via spores. Many of their species are admired for their aesthetics.

However, despite being excellent bioindicators that allow for scientists and decision-makers to monitor the state of ecosystems in the face of climate change and global biodiversity crisis, these species are too often overlooked due to their relatively small size and lack of vivid colours.

Spike moss (*Selaginella versicolor*) with a preference for very humid and shaded forests.

To bridge the existing gaps in the knowledge about the diversity of ferns and their allied species, while also seeking to identify the ways these plants select their habitats and react to the changes occurring there later on, a research team from Togo and France launched an ambitious biodiversity project in 2013. As for the setting of their long-term study, they chose Togo – an amazingly species-rich country in Western Africa, whose flora expectedly turned out to be hugely understudied.

Having concluded their fern project in 2017, scientists Komla Elikplim Abotsi and Kouami Kokou from the Laboratory of Forestry Research, University of Lomé, Togo, who teamed up with Jean-Yves Dubuisson and Germinal Rouhan, both affiliated with the Institute of Systematics Evolution and Biodiversity (UMR 7205), France, have their first findings published in a taxonomic paper in the open access Biodiversity Data Journal.

In this first-of-a-kind checklist of Togolese ferns, the researchers record as many as 73 species previously not known to inhabit the country, including 12 species introduced for horticultural purposes. As a result of their 4-year study, the pteridophyte diversity of Togo – a country barely taking up 56,600 km² – now counts a total of 134 species.

Still, the authors believe that there are even more species waiting to be discovered on both national and global level.

“Additional investigations in the difficult to access areas of the far north of the country, and Togo Mountains are still needed to fill possible biodiversity data gaps and enable decision-makers to make the right decisions,” say the researchers.

The triangular staghorn species *Platycerium stemaria* living on a coffee tree branch.

In addition to their taxonomic paper, the authors are also set to publish an illustrated guide to the pteridophytes of Togo, in order to familiarise amateur botanists with this fascinating biodiversity.

Original source:
Abotsi KE, Kokou K, Dubuisson J-Y, Rouhan G (2018) A first checklist of the Pteridophytes of Togo (West Africa). Biodiversity Data Journal 6: e24137. https://doi.org/10.3897/BDJ.6.e24137

Audit finds biodiversity data aggregators ‘lose and confuse’ data

In an effort to improve the quality of biodiversity records, the Atlas of Living Australia (ALA) and the Global Biodiversity Information Facility (GBIF) use automated data processing to check individual data items. The records are provided to the ALA and GBIF by museums, herbaria and other biodiversity data sources.

However, an independent analysis of such records reports that ALA and GBIF data processing also leads to data loss and unjustified changes in scientific names.

The study was carried out by Dr Robert Mesibov, an Australian millipede specialist who also works as a data auditor. Dr Mesibov checked around 800,000 records retrieved from the Australian Museum, Museums Victoria and the New Zealand Arthropod Collection. His results are published in the open access journal ZooKeys, and also archived in a public data repository.

“I was mainly interested in changes made by the aggregators to the genus and species names in the records,” said Dr Mesibov.

“I found that names in up to 1 in 5 records were changed, often because the aggregator couldn’t find the name in the look-up table it used.”

Another worrying result concerned type specimens – the reference specimens upon which scientific names are based. On a number of occasions, the aggregators were found to have replaced the name of a type specimen with a name tied to an entirely different type specimen.

The biggest surprise, according to Dr Mesibov, was the major disagreement on names between aggregators.

“There was very little agreement,” he explained. “One aggregator would change a name and the other wouldn’t, or would change it in a different way.”

Furthermore, dates, names and locality information were sometimes lost from records, mainly due to programming errors in the software used by aggregators to check data items. In some data fields the loss reached 100%, with no original data items surviving the processing.

“The lesson from this audit is that biodiversity data aggregation isn’t harmless,” said Dr Mesibov. “It can lose and confuse perfectly good data.”

“Users of aggregated data should always download both original and processed data items, and should check for data loss or modification, and for replacement of names,” he concluded.

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Original source:

Mesibov R (2018) An audit of some filtering effects in aggregated occurrence records. ZooKeys 751: 129-146. https://doi.org/10.3897/zookeys.751.24791

Poison ivy an unlikely hero in warding off exotic invaders?

Dozens of studies have looked at the effects of Japanese knotweed on natural communities in Europe and North America. Yet Bucknell University professor Chris Martine still felt there was something important to learn about what the plant was doing along the river in his own backyard.

“The more time I spent in the forests along the Susquehanna River, the more it seemed like something was really going wrong there,” said Martine. “In addition to the prevalence of this single invasive species, it looked like the very existence of these forests was under threat.”

What Martine noticed was similar to what local nature lovers and biologists with the Pennsylvania Natural Heritage Program were also starting to see: these forests, specifically those classified as Silver Maple Floodplain Forests, were not regenerating themselves where knotweed had taken a foothold.

In a new study published in the open access Biodiversity Data Journal, Martine and two recent Bucknell alumni conclude that Japanese knotweed has not only excluded nearly all of the native understory plant species in these forests, but it has prevented the trees already established in the canopy from leaving behind more of themselves.

“If you were to fly over these forests, or even look at a Google Earth image, you’d see a nice green canopy along the river consisting of mature silver maples, river birches, and sycamores,” explained Martine. “But below that canopy there is almost nothing for tens of feet before you reach an eight-to-twelve-foot-tall thicket of knotweed. Few new trees have been able to grow through that in the last 50-60 years and our surveys found that seedlings of these species are quite rare.”

The authors suggest that as mature trees die of natural causes over the next several decades and are not replaced, these systems will shift from tree-dominated riverbank habitats to “knotweed-dominated herbaceous shrublands” incapable of supporting a rich diversity of insects, birds, and other wildlife. Loss of trees in these habitats could likely also lead to riverbank erosion and increase the severity of flood events.

The few places where knotweed has not taken over offer a bit of hope, however, from an unlikely hero: poison-ivy, which Martine calls “perhaps the least popular plant in America.”

“What we see in the data is that poison-ivy often trades understory dominance with knotweed. That is, when knotweed isn’t the big boss, poison-ivy usually is. The difference is that whereas knotweed knocks everyone else out of the system, poison-ivy is more of a team player. Many other native plants can co-occur with it and it even seems to create microhabitats that help tree seedlings get established.”

The prevalence of poison-ivy in these sites didn’t go unnoticed by undergraduate Anna Freundlich, who collected most of the plant community data — more than 1,000 data points — in a single summer as a research fellow.

“Anna developed a pretty serious methodology for avoiding a poison-ivy rash that included long sleeves, long pants, gloves, duct tape, and an intense wash-down protocol,” said her research advisor, “and even after crawling through the plant for weeks she managed to never once get a rash.”

Martine cautions against too much optimism regarding the chances of one itch-inducing native plant saving the day, however.

“Righting this ship is going to require eradicating knotweed from some of these sites, and that won’t be easy work. It will take some hard manual labor. But it’s worth doing if we want to avoid the imminent ecological catastrophe. These forests really can’t afford another half-century of us letting knotweed run wild.”

Freundlich is a now pursuing a Master’s degree in plant ecology at the University of Northern Colorado. Lead author Matt Wilson, a Bucknell Master’s student at the time of the study who analyzed the dataset, now works for the Friends of the Verde River in Cottonwood, AZ.

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Original source:

Wilson M, Freundlich A, Martine C (2017) Understory dominance and the new climax: Impacts of Japanese knotweed (Fallopia japonica) invasion on native plant diversity and recruitment in a riparian woodland. Biodiversity Data Journal 5: e20577. https://doi.org/10.3897/BDJ.5.e20577

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About Japanese knotweed:

Japanese knotweed is considered to be one of the toughest, most damaging and insidious plants in the world. Native to East Asia, the species has already established successfully in many parts throughout North America and Europe, where it can easily grow and invade private properties and homes. It is hardy enough to penetrate patios, house foundations and concrete. Given it spreads easily and can grow underground to a depth of 3 metres with a horizontal range of up to 7 metres, it is extremely difficult to eradicate and its treatment requires special attention. To find advice on recognition, hazards and treatment, you can check out The Ultimate Japanese Knotweed Guide.

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