A year of biodiversity: Top 10 new species of 2021 from Pensoft journals, Part 1

With 2022 round the corner, we thought we’d start off the celebrations by looking back to some the most memorable discoveries of 2021. And what a year it has been! Many new species made their debuts on the pages of Pensoft journals – here’s our selection of the most exciting animals, plants and fungi that we published in 2021.

With 2022 round the corner, we thought we’d start off the celebrations by looking back to some the most memorable discoveries of 2021. And what a year it has been! Many new species made their debuts on the pages of Pensoft journals – here’s our selection of the most exciting animals, plants and fungi that we published in 2021.

10. The delicious wild oak mushroom

It’s amazing that edible species, long known to local communities, can still present a novelty for science. This was the case with Cantharellus veraecrucis, a chanterelle from – that’s right, Veracruz, Mexico.

During the rainy season, locals harvest this mushroom from tropical oak forests to sell it or enjoy it as a delicacy; this is probably why they’ve dubbed it “Oak mushroom”.

Published in: MycoKeys

9. The master of disguise

If you ever see a leaf insect, there’s a good chance you won’t notice it – these little critters are masters of camouflaging.

This picture was taken in 2014, when Jérôme Constant and Joachim Bresseel from the Royal Belgian Institute of Natural Sciences were enjoying a night walk in Vietnam’s Nui Chua National Park. It wasn’t until this year, though, that this beauty got its own scientific name: Cryptophyllium nuichuaense. Named after the park where it was found, it is one of 13 new species of leaf insects described in our journal ZooKeys this February.

This leaf insect, like many others, is endemic to Vietnam. This is why the researchers who found itcall for the creation of more protected areas in order to keep this precious biodiversity intact.

Published in: ZooKeys

8. The Neil Gaiman spider

Unlike most spiders, trapdoor spiders don’t use silk to make a web. Instead, they live in burrows lined with silk that they cover with a “trapdoor”. They are relatively widely spread, but you’d rarely encounter one out in the open, because they spend most of their lives underground.

This is probably why arachnologists and spider lovers the world over got so excited when Dr. Rebecca Godwin (Piedmont University, GA) and Dr. Jason Bond (University of California, Davis, CA) described 33 new species of trapdoor spiders from the genus Ummidia – in addition to the 27 already known.

Dr. Rebecca Godwin talks to L. Brian Patrick about her discovery of 33 new species of trapdoor spiders on his podcast New Species.

One of the 33 is Ummidia neilgaimani, named after fantasy and horror writer Neil Gaiman. A particular favorite of Dr. Godwin, Gaiman is the author of a number of books with spider-based characters. His novel American Gods features a character based on the West African spider god Anansi and a World Tree “one hour south of Blacksburg,” not far from the type locality of this species. He’s also part of the documentary Sixteen Legs, in his own words “An amazing film about Tasmanian cave spider sex.”

“I think anything we can do to increase people’s interest in the diversity around them is worthwhile and giving species names that people recognize but that still have relevant meaning is one way to do that,” says Dr. Godwin.

Published in: ZooKeys

7. The deadly Chinese-goddess snake

Bungarus suzhenae was only described as a new species this year, but its reputation preceded it – in a bad way. Researchers were already familiar with a notorious black-and-white banded krait that bit herpetologists on expeditions in Myanmar and China – in one infamous case, to death. After extensive morphological and phylogenetical analysis, the researchers were finally able to confirm it as new to science.

The story behind B. suzhenae’s name is interesting, too: it was named after a character from the traditional Chinese myth ‘Legend of White Snake’. The powerful snake goddess Bai Su Zhen is to this day regarded as a symbol of true love and good-heartedness in China. 

Snakebites from kraits – including this one – are known to have a high mortality. This is why the new knowledge on B. suzhenae and its description as a new species are essential to the research on its venom and an important step in the development of antivenom and improved snakebite treatment.

Published in: ZooKeys

6. The ephemeral fairy lanterns

Commonly known as “fairy lanterns”, plants of the genus Thismia are very rare and small in size. They are mycoheterotrophic, which means they live in close association with fungi from which they acquire most of their nutrition. They’re also very elusive, growing in dark, remote rainforests, and visible only when they emerge to flower and set seed after heavy rain.

In fact, researchers were only able to find one specimen of the new T. sitimeriamiae, which they discovered in the Terengganu State of Malaysia – the rest of the population had been destroyed by wild boars.

Just discovered, T. sitimeriamiae may already be threatened by extinction – which is why the research team that discovered it suggest that this exceptionally rare plant is classified as Critically Endangered.

Published in: PhytoKeys

Part 2 coming soon – stay tuned!

Delicious discoveries: Scientists just described a new onion species from the Himalaya

While the onion, garlic, scallion, shallot and chives have been on our plates for centuries, becoming staple foods around the world, their group, the genus Allium, seems to be a long way from running out of surprises. Recently, a group of researchers from India described a new onion species from the western Himalaya region, long known to the locals as “jambu” and “phran”, in the open-access journal PhytoKeys.

The genus Allium contains about 1,100 species worldwide, including many staple foods like onion, garlic, scallion, shallot and chives. Even though this group of vegetables has been making appearances at family dinners for centuries, it turns out that it is a long way from running out of surprises, as a group of researchers from India recently found out.

The flower of Allium negianum

In 2019, Dr. Anjula Pandey, Principal Scientist at ICAR-National Bureau of Plant Genetic Resources in New Delhi, together with scientists, Drs K Madhav Rai, Pavan Kumar Malav and S Rajkumar, was working on the systematic botany of the genus Allium for the Indian region, when the team came across plants of what would soon be confirmed as a new species for science in the open-access journal PhytoKeys.

The plant, called Allium negianum, was discovered in the Indo-Tibetan border area of Malari village, Niti valley of Chamoli district in Uttarakhand. It grows at 3000 to 4800 m above sea level and can be found along open grassy meadows, sandy soils along rivers, and streams forming in snow pasture lands along alpine meadows (locally known as “bugyal” or “bugial”), where the melting snow actually helps carry its seeds to more favourable areas. With a pretty narrow distribution, this newly described speciesis restricted to the region of western Himalaya and hasn’t yet been reported from anywhere else in the world. The scientific name Allium negianum honours the late Dr. Kuldeep Singh Negi, an eminent explorer and Allium collector from India.

Although new to science, this species has long been known under domestic cultivation to local communities. While working on this group, the research team heard of  phran, jambu, sakua, sungdung, and kacho – different local names for seasoning onions. According to locals, the one from Niti valley was particularly good, even deemed the best on the market.

The bulb and underground parts of Allium negianum.

So far only known from the western Himalaya region, Allium negianum might be under pressure from people looking to taste it: the researchers fear that indiscriminate harvest of its leaves and bulbs for seasoning may pose a threat to its wild populations.

Research article:

Pandey A, Rai KM, Malav PK, Rajkumar S (2021) Allium negianum (Amaryllidaceae): a new species under subg. Rhizirideum from Uttarakhand Himalaya, India. PhytoKeys 183: 77-93. https://doi.org/10.3897/phytokeys.183.65433

Two new tree species discovered in Colombia

Trees of the genus Otoba have small, foul-smelling flowers coloured in yellow or greenish yellow, and round, aromatic fruits. Toucans, monkeys, or small terrestrial animals sometimes feed on their fruits, while herbivorous insects have developed a taste for their leaves. Part of the nutmeg family, Otoba trees are widely distributed from Nicaragua to Brazil, with as many as nine species native to Colombia.

Fruits of Otoba from Osa Peninsula, Costa Rica. Photo by Reinaldo Aguilar

Despite this apparent abundance, though, scientific knowledge on their biology is very limited.

Thanks to researchers from the Louisiana State University and the Missouri Botanical Garden, we now know more about these interesting trees, as Daniel Santamaría-Aguilar and Laura P. Lagomarsino recently described two new species of Otoba in the open-access, peer-reviewed journal PhytoKeys.

Even though the COVID-19 pandemic meant limited access to physical specimens, the research team were able to identify the two new species while investigating herbaria samples. This discovery helps clear some taxonomic confusions in the genus, as both of these new species had often been mistaken for other Otoba members.

The newly described Otoba scottmorii and Otoba squamosa can be found in Colombia’s Antioquia department, growing in premontane and humid forests. Known from the premontane forests of Cordillera Occidental in Colombia, Otoba squamosa grows at 1330–1450 m, while Otoba scottmorii, locally known as Cuángare otobo, grows in the humid forests in the Department of Antioquia, northwestern Colombia.

Staminate flowers of Otoba from Osa Peninsula, Costa Rica. Photo by Reinaldo Aguilar

The scientific name scotmorii is a tribute to Dr. Scott A. Mori (1941–2020), “a wonderful person and skilled botanist; a dedicated explorer of Central and South America humid forests (where this species occurs), especially in the Guianas and the Amazon basin; and an authority on Neotropical Lecythidaceae,” who inspired and personally supported Daniel Santamaría-Aguilar in his botanical work.

Because their habitats are threatened by deforestation, both tree species are preliminarily assessed as Endangered according to the criteria of the International Union for Conservation of Nature.

Research article:

Santamaría-Aguilar D, Lagomarsino LP (2021) Two new species of Otoba (Myristicaceae) from Colombia. PhytoKeys 178: 147-170. https://doi.org/10.3897/phytokeys.178.64564

Rare new orchid species just discovered in the Andes

Three new endemic orchid species were discovered in Ecuador and described in the open-access, peer-reviewed journal PhytoKeys. Lepanthes microprosartima, L. caranqui and L. oro-lojaensis are proof that Ecuador – one of the world’s megadiverse countries – hides much more biodiversity waiting to be explored.

For its size, Ecuador has an impressive biological diversity that harbours a unique set of species and ecosystems, many of them endemic or threatened. Because of this great biodiversity, most studies still focus on recording species richness and very little is known about how these species actually interact. This is why in 2017 Dr Catherine H. Graham from the Swiss Federal Institute for Forest, Snow and Landscape Research WSL, with support from the European Research Council and local NGO Aves y Conservation, initiated an ambitious project in the northwestern Andes of Ecuador to study the ecology of plant-hummingbird interactions along an altitudinal and land-use gradient.

Lepanthes oro-lojaensis. Photo by Diego Francisco Tobar Suàrez

To this end, researchers established 18 transects in areas of well-preserved cloud forest and sites at different altitude and with different levels of disturbance, and visited them monthly to count the flowers that attract hummingbirds and to place time-lapse cameras in flowering plants.

Lepanthes microprosartima. Photo by Diego Francisco Tobar Suàrez

Several new species to science were discovered during the intensive botanical work of identifying the nearly 400 plant species recorded by the surveys and cameras. One of them is a new orchid species called Lepanthes microprosartima.

Found on the western slopes of Pichincha volcano in northern Ecuador, L. microprosartima is endemic to the Yanacocha and Verdecocha reserves, where it grows at 3200 to 3800 m above sea level in evergreen montane forest – remarkably, this species can thrive even under deep shade in the forest.

Over three years of monitoring, only 40 individuals of L. microprosartima were found, which suggests it is a rare species. Because of this, and because it is only found in a small area, researchers preliminarily assessed it as Critically Endangered according to IUCN criteria.

Lepanthes caranqui. Photo by Diego Francisco Tobar Suàrez

Within the same hummingbird monitoring project, another new orchid – Lepanthes caranqui – was discovered in eastern Pichincha. Around the same time, a different research group from the Pontifical Catholic University of Ecuador found the same species in Imbabura. While in Imbabura it was found growing in páramo, with small groups on roadside embankments, in Pichincha it grew in evergreen montane forest, on top of tree trunks or lower branches, in the company of other orchid species. Its name, Lepanthes caranqui, honors the Caranqui culture that historically occupied the areas where this plant grows.

Lepanthes oro-lojaensis. Photo by Diego Francisco Tobar Suàrez

But the wonders of Ecuadorean biodiversity don’t stop there – a research project of Ecuador’s National Institute of Biodiversity found another new species, as small as 3 cm, in the southwest of El Oro. Lepanthes oro-lojaensis was actually discovered on the border between El Oro and Loja provinces, hence its name. It was only found from one locality, where its populations are threatened by cattle ranching, fires, plantations of exotic species, and the collection of shrubs as firewood. This is why researchers believe it should be listed as Critically Endangered according to IUCN criteria.

These additions to the Ecuadorean flora are all described in the open-access, peer-reviewed journal PhytoKeys. They are proof that Ecuador – one of the world’s megadiverse countries – hides much more biodiversity waiting to be explored.

Original source:

Suarez FT, López MF, Gavilanes MJ, Monteros MF, García TS, Graham CH (2021) Three new endemic species of Lepanthes (Orchidaceae, Pleurothallidinae) from the highlands of Ecuador. PhytoKeys 180: 111-132. https://doi.org/10.3897/phytokeys.180.62671

Guest Blog Post: Researchers split the birdcatcher trees (genus Pisonia) into three

Large Cabbage trees (Pisonia grandis) dominate the landscape of a small island in the Pacific Ocean
Photo by Jean-Yves Meyer (Délégation à la Recherche de Polynésie Française, Tahiti, French Polynesia)

Guest blog post by Marcos Caraballo

The birdcatcher trees – genus Pisonia – are infamous for trapping birds with their super-sticky seed pods that would frequently entangle the body of the ‘victim’. Left flightless, the poor feathered creatures eventually die either from starvation or fatigue, or predators. Similarly notorious are the birdcatcher trees for botanists, who have been baffled by their complicated classification for the last three centuries. 

Here’s why myself and graduate student Elson Felipe Rossetto of the Universidade Estadual de Londrina (Brazil) decided to take up the untangling of this issue with our recent taxonomic studies. You can find our research paper published in the open-access scholarly journal PhytoKeys.

Ripe fruits (anthocarps) of the Birdlime tree (Ceodes umbellifera)
Photo by Ching-I Peng [deceased]

We reestablished two genera: Ceodes and Rockia, where both had been previously merged under the name of Pisonia. Now, as a result, there are three distinct lineages of birdcatcher trees from the islands of the Pacific and Indian Oceans: Ceodes, Pisonia, and Rockia.

“Previous molecular studies on Pisonia species from around the world showed that species were clustered into three major groups, and here we assign names for each of them. With this new classification, a large number of the species known as Pisonia will be henceforth named Ceodes. This includes the Parapara (Ceodes brunoniana) and the Birdlime (Ceodes umbellifera) trees, both native to many islands, including Hawaii and New Zealand. They are commonly planted in gardens for their lush and sometimes variegated foliage, as well as their fragrant white flowers. However, the Cabbage tree (Pisonia grandis) will still be technically known as Pisonia.”

adds the study’s lead author Felipe Rossetto.
Male (staminate) showy flowers of the Birdlime tree (Ceodes umbellifera)
Photo by Joel Bradshaw (Far Outliers, Honolulu, Hawaii)

Birdcatcher trees have generated much controversy in the popular media because of their seed pods (technically called “anthocarps”) secreting a sticky substance that glues them to the feathers of seabirds or other animals for dispersal. Sometimes, though, too many seed pods can harm or kill birds, especially small ones, by weighing them down and rendering them flightless. This macabre practice has led to many controversies and local campaigns aiming to remove the trees, even illegally.

Brown noddy (Anous stolidus) covered with the sticky fruits (anthocarps) of the Cabbage tree (Pisonia grandis)
Photo by Jean-Yves Meyer (Délégation à la Recherche de Polynésie Française, Tahiti, French Polynesia)

In spite of their forbidding reputation, however, we would like to stress that birdcatcher trees have positive effects on ecosystems and are important components of vegetation, especially for small islands. Sadly, there are many endemic and already endangered species of birdcatcher trees that only exist on a few small islands, where they are effectively placed at the mercy of local people.

Many species of birdcatcher trees are large and, thereby, tolerate harsh environments like seafronts and rocky cliffs, making them prime nesting spots for seabirds. Birdcatcher trees are also ecologically curious and could be regarded as keystone species in small islands, because their soft branches can sustain many types of invertebrates; their flowers are an important food source for bees and ants; their dense leaf litter nourishes the soil; and their roots have intimate interaction with native underground fungi (mycorrhiza).

All in all, clarifying the taxonomy of the birdcatcher trees is the first step to understanding how many species exist and how they relate to each other. 

Although most people relate birdcatcher trees with beaches and coastal habitats, there are species that are only found in mountains or rainforests. For example, the species now allocated to the genus Rockia is endemic to the Hawaiian archipelago. These are small trees able to grow in dry to mesic mountain forests. Using our new classification, future studies can explore in detail the hidden diversity of these enigmatic plants, and find out how trees with high dispersal capabilities evolve into species endemic to small island ecosystems.

Cabbage trees (Pisonia grandis) are important components of the vegetation in small islands due to their massive size
Photo by Jean-Yves Meyer (Délégation à la Recherche de Polynésie Française, Tahiti, French Polynesia)

About the author:

Marcos A. Caraballo-Ortiz is a research associate at the Smithsonian Institution (Washington, D.C., United States). His research interests include plant systematics and ecology, with a focus on flora of the Caribbean Islands. Dr. Caraballo-Ortiz has experience studying the taxonomy of several groups of tropical plants, with a particular interest in neotropical Mistletoes (Loranthaceae, Santalaceae, Viscaceae) and the Four O’Clock family (Nyctaginaceae). 

For more information about his projects, visit marcoscaraballo.com.

Research paper:

Rossetto EFS, Caraballo-Ortiz MA (2020) Splitting the Pisonia birdcatcher trees: re-establishment of Ceodes and Rockia (Nyctaginaceae, Pisonieae). PhytoKeys 152: 121-136. https://doi.org/10.3897/phytokeys.152.50611

Issue #150 of PhytoKeys marks a decade of revolutionising open plant systematics

So, it’s been ten years and exactly 150 issues since what currently is known as one of the top scholarly journals in plant systematics was launched with the aim to address four key challenges in research accessibility, all of which, however, remain all too relevant still:

  • Digitisation of academic research;
  • Open Access as a publishing model; 
  • Linkage of data available from electronic registers, indices and aggregators to bring together essential information about species;
  • Semantic markup and semantic enhancements to facilitate access to scientific published biological works. 

Nevertheless, we should acknowledge that the past decade has marked a great step forward, with journals like PhytoKeys proud to have assumed the role of a pioneering example in scholarly publishing.

PhytoKeys represented for me a way to bring the results of science to everyone, especially in countries rich in biodiversity but poor in resources to pay huge journal fees. I am so happy that the journal thrives, and continues to strive to bring the knowledge created by botanists from around the world to those who need it most, free from barriers and in an open and linked way,”

says Dr Sandy Knapp, Editor-in-Chief of PhytoKeys and Merit Researcher at the Natural History Museum of London

For ten years now, PhytoKeys has continued to attract increasing interest from researchers looking to publish their novel findings in the domain of botany where they can be openly and freely shared. Indeed, the journal’s stats clearly demonstrate the exponential growth of manuscripts submitted!

Manuscripts submitted (blue) vs. articles published (red) since the launch of PhytoKeys.
Accessed on 19 May 2020.

PhytoKeys continues to push the envelope on innovative publishing in plant taxonomy.  So many more species to describe and understand, while each day time gets shorter for discovering them.  We need everyone on-board to accelerate our efforts,”

says Dr W. John Kress, Editor-in-Chief of PhytoKeys and  the vice-president for science at the Smithsonian National Museum of Natural History (Washington, D.C.)

Data Publishing Innovations

A standard appendix template for primary biodiversity data was recently introduced across Pensoft’s journals to provide direct harvesting and conversion to interlinked FAIR data. Learn more on our blog.

Alongside other biodiversity data-publishing journals on the Pensoft platform, PhytoKeys is also widely recognised for its commitment when it comes to data papers, whose purpose is to describe and contextualise datasets that are already available perhaps elsewhere. 

Data audit workflow provided for data papers submitted to Pensoft journals.

An excellent example for taking care after data quality, hence accessibility and reusability, is the mandatory data audit workflow introduced in early 2019. Have a look at this case study following the experience of University of Cordoba’s scientists Dr Gloria Martínez-Sagarra and Prof Juan Antonio Devesa, who described the herbarium dataset for the vascular plants in COFC.

What’s HOT on PhytoKeys?

Six special issues published in PhytoKeys in 2020.

This year, we have already seen the publication of six special issues in PhytoKeys, including the 150th issue, presenting the official report on the discussions and decisions of the week-long Nomenclature Section held in the week before the XIX International Botanical Congress held in Shenzhen, China, in 2017. This issue will be the historical record for this ground-breaking meeting, where algal, fungal and plant naming rules were changed to increase participation.

In the past ten years, the journal is proud to have published a total of forty special issues, in order to put together big chunks in the puzzle of plant life on Earth.

1. XIX International Botanical Congress, Shenzhen: report of the Nomenclature Section, 17th to 21st July 2017 (Issue 150)

Published as the anniversarial 150th issue, the official report on the discussions and decisions of the ten sessions of the Nomenclature Section of the XIX International Botanical Congress, paints “a true and lively picture of the event, retaining the atmosphere of goodwill and humour that infused the meeting”. 

The meeting, held in Shenzhen, China, in 2017, brought together 155 registered members of the Section representing 30 countries, of whom 71 carried 427 institutional votes from 166 institutions in 41 countries, making a total of 582 possible votes representing 44 countries.  The main result of the Section’s discussions and decisions is the Shenzhen Code.

2. An annotated checklist of the coastal forests of Kenya, East Africa, (Issue 147)

A collaboration between research teams from China and Kenya resulted in an extensive and detailed checklist of vascular plants inhabiting the coastal forests of Kenya, in order to facilitate adequate risk assessments. Despite being existent for millions of years and well-known as a biodiversity hotspot, these forests are under anthropogenic pressure that has already led to their serious fragmentation. Nevertheless, these can still be saved before meeting the fate of other forest patches along the coasts of Africa, which rarely exceed 5 km2.

3. A synoptic review of the aloes (Asphodelaceae, Alooideae) of KwaZulu-Natal, an ecologically diverse province in eastern South Africa (Issue 142)

In another major study dealing with the astonishing biodiversity of African coasts, researchers from South Africa compiled the first ever atlas of aloe occurrence in KwaZulu-Natal (South Africa). Their monograph enlists a total of four genera and 49 taxa, where fourteen are endemic and eleven near-endemic to the province that spans over 92 290 km2.

4. Vascular plants of Victoria Island (Northwest Territories and  Nunavut, Canada): a specimen-based study of an Arctic flora (Issue 141)

To bridge the gap in knowledge about vascular flora of Victoria Island – the eighth largest island in the world, where plant diversity remains very poorly explored – Canadian scientists studied nearly 1,000 specimens from a total of 7,031 unique collections. The resulting monograph brings together 38 families, 108 genera, 272 species, and 17 additional taxa, which are to serve as a new baseline for continued exploration of the vascular flora of Victoria Island.

5. Plant diversity of Southeast Asia-II (Issue 138)

Despite hosting four global biodiversity hotspots, the plants of Southeast Asia are yet to be fully grasped by scientific accounts. Meanwhile, this rich diversity is under a serious threat posed by rapid economic development and population growth. This special issue, published in PhytoKeys in January, reports on the findings of the last six investigations of The Belt and Road Initiative (BRI): a long-term programme, whose mission is to connect the world with the aim of increasing trade and economic growth and accelerating regional integration, while preserving biodiversity and promoting sustainable development in Southeast Asia.

6. Scorzonera sensu lato (Asteraceae, Cichorieae) – taxonomic reassessment in the light of new molecular phylogenetic and carpological analyses (Issue 137)

The first comprehensive sampling of the flowering genus Scorzonera in its widest sense and all other genera recognised in the subtribe Scorzonerinae of the dandelion tribe (Cichorieae) was reported by a team of German and Russian scientists, in order to resolve long-standing debates over the circumscription of the genus and its 180–190 species. In their paper, the researchers provide a re-evaluation of Scorzonera and other related genera, based on morphological, including anatomical and carpological, and extended molecular phylogenetic analyses.

Top Pop Plants!

Last time around, we celebrated the 100th issue of PhytoKeys with a blog post recalling the five most exciting new species published in the journal to that date (21 June 2018). 

So, to follow this cool tradition, it only makes sense to take a look back at the TOP 5 most talked about discoveries published in PhytoKeys since then. 
Here are the top 5 according to the data available from the public attention tracker Altmetric, in descending order:

5. A common large and widely used palm in Cameroon went nameless

The overlooked giant: the newly described palm tree Raphia zamiana.
Photo by Thomas L.P. Couvreur.

A palm tree large in size and numbers that grows along the roadside is hard to stay under cover, isn’t it? Not this one, though. 

Found in southern Cameroon and western Gabon, palm trees that the local people call “Zam” have long been used in the region for a range of purposes, including timber in construction, fruits – for consumption and medicine, and sap – in wine tapping. 

However, it was only in 2018 that the international research team, led by  Suzanne Mogue Kamga of the Yaoundé I University (Cameroon) identified the species as missing in the scientific literature. They made the discovery during a three-year-long extensive field survey in Gabon, Cameroon, Republic of Congo and the Democratic Republic of Congo. 

Find more on our blog

Research paper: 

Kamga SM, Niangadouma R, Stauffer FW, Sonké B, Couvreur TLP (2018) Two new species of Raphia (Palmae/Arecaceae) from Cameroon and Gabon. PhytoKeys 111: 17-30. https://doi.org/10.3897/phytokeys.111.27175 

4. Massive monograph for the morning glories of the New World 

Sweet potato (Ipomoea batatas) growing as a weed in a waste ground, San Ramon, Peru.
Photo by Robert Scotland.

To avoid major overlooking of relatives of the sweet potato and the moonflower, similarly to the case of the palm tree we just told you about, here, a research team from the University of Oxford undertook a massive, even painstaking task, involving hundreds of species and times more specimens, in addition to numerous and dispersed herbaria, where they needed to find the specimens, and scattered, often obscure literature.

As a result, they listed a total of 425 species representing all members of the largest genus within the morning glory family (Convolvulaceae): Ipomoea, found in the New World. Furthermore, they provided details, including distributional data for each of those plants. 

Importantly, their study relies on the “foundation monograph” approach the authors had previously invented to bring together standard techniques with the use of online digital images and molecular sequence data. Thereby, the scientists were able to focus on species-level taxonomic problems across the entire distribution range of individual species.

Find more on our blog.

Research paper:

Wood JR.I, Muñoz-Rodríguez P, Williams BR.M, Scotland RW (2020) A foundation monograph of Ipomoea (Convolvulaceae) in the New World. PhytoKeys 143: 1-823. https://doi.org/10.3897/phytokeys.143.32821

3. Blood-red aloe waited for an ID card by the roads of Somaliland

Inflorescence branch and flowers of Aloe sanguinalis. On the left there is the sap as it develops to the rich dark red color, which gave the name of the new species.
Photo by Barkworth M, et al.

So, being large and commonly utilised is no guarantee to attract formal recognition in the world of plants, but a striking colouration could surely do better, you might be thinking.

Think again. A species of conspicuous blood-red aloe growing along the roads of Somaliland, spectacular for its large clumps and sap, which once released, quickly turns from yellow to bright red and then to dark-red or reddish-brown, remained unknown to science until last year. 

Just like in the case with the African palm, the locals were well aware of the “bloody” aloe and, apparently, its specificity. All along they’ve been calling it “Dacar cas” or “Red aloe”.

In fact, the discovery of what we now shall refer to as Aloe sanguinalis (from sanguineus, Latin for blood, in reference to its one-of-a-kind red sap) starts with co-author Ahmed Awale, a leading Somaliland environmentalist, who spotted the large, reddish clumps of the plant, while driving through the country on behalf of Candlelight, an NGO focused on the environment, education, and health.

Find more on our blog.

Research paper:

Barkworth ME, Awale AI, Gelle FJ (2019) Dacar Cas/Somali Red Aloe: a new species of Aloe (Asphodelaceae) from Somaliland. PhytoKeys 117: 85-97. https://doi.org/10.3897/phytokeys.117.28226     

2. The “oldest bamboo” fossil from Eocene Patagonia turned out to be a conifer

The holotype of the species Retrophyllum oxyphyllum (comb. nov.), previously thought to be the oldest known bamboo.
Photo by Peter Wilf.

Unlike the stories above, this one deals with a species scientists thought they knew everything about. 

Originally named Chusquea oxyphylla, a fossilised leafy branch dated to the early Eocene and discovered in Patagonia (South America) back in 1941, was thought to be the oldest bamboo fossil and the main evidence for a Gondwanan origin of bamboos ever since.

However, upon close examination, Dr. Peter Wilf from Pennsylvania State University revealed the historic specimen was in fact a conifer. As a result, the species was renamed to Retrophyllum oxyphyllum.

Find more on our blog.

Research paper:

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 

1. The Australian bush tomato that can switch between sexes

The unusual with its breeding system fluidity new to science bush tomato species Solanum plastisexum.
Photo by Chris Martine.

Here comes the #1 in most talked about of the studies published in PhytoKeys since June 2018. This is a new species of Australian bush tomato, named Solanum plastisexum, whose remarkable sexual fluidity means that plants switch between breeding systems – from bearing a mixture of male and female flowers, to having only male or female flowers, to having hermaphroditic flowers – throughout their lives. 

“For the most part, a given plant species will stick to one primary and predictable type of sexual expression,” explains senior author of the study Dr Chris Martine, a professor of botany at Bucknell University, “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 considering the scope of life on Earth, the notion of a constant sexual binary consisting of distinct and disconnected forms is, fundamentally, a fallacy,” conclude the authors.

Find more on our blog.

Research paper: 

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

Read the story of Solanum plastisexum in The New York Times.

Major advances in our understanding of New World Morning Glories

John Wood of the Oxford team members collecting plants in Bolivia
Photo by BRM Williams

A major advance in revealing the unknown plant diversity on planet Earth is made with a new monograph, published in the open-access, peer-reviewed journal PhytoKeys. The global-wide study, conducted by researchers at the University of Oxford, lists details about each of the 425 New World species in the largest genus within the family of morning glories, thanks to an all-round approach combining standard, modern and new-generation identification techniques. 

The family of morning glories, also known as bindweeds, whose scientific name is Convolvulaceae, includes prominent members like the sweet potato and ornamental plants such as the moonflower and the blue dawn flower. In fact, one of the key conclusions, made in the present work, is that within this plant group there are many other species, besides the sweet potato, that evolved storage roots long before modern humans appeared on Earth. Furthermore, most of those are yet to be evaluated for economic purposes.

Sweet potato (Ipomoea batatas) growing as a weed in a waste ground, San Ramon, Peru
Photo by Robert Scotland

To make their findings, the research team of John Wood, Dr Pablo Muñoz Rodríguez, Bethany R.M. Williams and Prof Robert Scotland applied the “foundation monograph” concept that they had developed for similarly diverse and globally distributed, yet largely understudied groups. Usually, such groups with hundreds of species have never been surveyed across their entire geographical range, which in turn results in the existence of many overlooked new species or species wrongly named.

As a result, the monograph adds six new to science species and establishes nine new subspecies, previously recognised as either distinct species or varieties. The publication also cites all countries where any of those 425 morning glories occurs. In order to provide detailed knowledge about their identities and ecologies, the authors also produced over 200 illustrative figures: both line drawings and photos.

In their study, the scientists also investigate poorly known phenomena concerning the genus. For instance, the majority of the plants appear to originate from two very large centres, from where they must have consequently radiated: the Parana region of South America and the Caribbean Islands. Today, however, a considerable amount of those species can be found all around the globe. Interestingly, the team also notes a strong trend for individual species or clades (separate species with a common ancestor) to inhabit disjunct localities at comparable latitudes on either side of the tropics in North America and South America, but not the Equator.

Prof Robert Scotland (University of Oxford) with the evolutionary tree of Ipomoea that includes 2000 specimens sequenced for DNA
Photo by John Baker

The monograph exemplifies the immense value of natural history collections. Even though the researchers have conducted fieldwork, most of their research is based on herbarium specimens. They have even managed to apply DNA sequencing to specimens over 100 years old. The publication also provides detailed information about the characteristics, distribution and ecology of all the species. It is illustrated with over 200 figures, both line drawings and photos.

“A major challenge in monographing these groups is the size of the task given the number of species, their global distribution and extensive synonymy, the large and increasing number of specimens, the numerous and dispersed herbaria where specimens are housed and an extensive, scattered and often obscure literature,”

comment the scientists.

“Unlike traditional taxonomic approaches, the ‘foundation monograph’ relies on a combination of standard techniques with the use of online digital images and molecular sequence data. Thereby, the scientists are able to focus on species-level taxonomic problems across the entire distribution range of individual species,”

they explained.


In a separate paper, published in Nature Plants last November, the research team provides further insights into how they have assembled the monograph and include all the molecular sequence data and phylogenetics produced during their work.


Original source:
Wood JR.I, Muñoz-Rodríguez P, Williams BR.M, Scotland RW (2020) A foundation monograph of Ipomoea (Convolvulaceae) in the New World. PhytoKeys 143: 1-823. https://doi.org/10.3897/phytokeys.143.32821

“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.

Data mining applied to scholarly publications to finally reveal Earth’s biodiversity

At a time when a million species are at risk of extinction, according to a recent UN report, ironically, we don’t know how many species there are on Earth, nor have we noted down all those that we have come to know on a single list. In fact, we don’t even know how many species we would have put on such a list.

The combined research including over 2,000 natural history institutions worldwide, produced an estimated ~500 million pages of scholarly publications and tens of millions of illustrations and species descriptions, comprising all we currently know about the diversity of life. However, most of it isn’t digitally accessible. Even if it were digital, our current publishing systems wouldn’t be able to keep up, given that there are about 50 species described as new to science every day, with all of these published in plain text and PDF format, where the data cannot be mined by machines, thereby requiring a human to extract them. Furthermore, those publications would often appear in subscription (closed access) journals.

The Biodiversity Literature Repository (BLR), a joint project ofPlaziPensoft and Zenodo at CERN, takes on the challenge to open up the access to the data trapped in scientific publications, and find out how many species we know so far, what are their most important characteristics (also referred to as descriptions or taxonomic treatments), and how they look on various images. To do so, BLR uses highly standardised formats and terminology, typical for scientific publications, to discover and extract data from text written primarily for human consumption.

By relying on state-of-the-art data mining algorithms, BLR allows for the detection, extraction and enrichment of data, including DNA sequences, specimen collecting data or related descriptions, as well as providing implicit links to their sources: collections, repositories etc. As a result, BLR is the world’s largest public domain database of taxonomic treatments, images and associated original publications.

Once the data are available, they are immediately distributed to global biodiversity platforms, such as GBIF–the Global Biodiversity Information Facility. As of now, there are about 42,000 species, whose original scientific descriptions are only accessible because of BLR.

The very basic principle in science to cite previous information allows us to trace back the history of a particular species, to understand how the knowledge about it grew over time, and even whether and how its name has changed through the years. As a result, this service is one avenue to uncover the catalogue of life by means of simple lookups.

So far, the lessons learned have led to the development of TaxPub, an extension of the United States National Library of Medicine Journal Tag Suite and its application in a new class of 26 scientific journals. As a result, the data associated with articles in these journals are machine-accessible from the beginning of the publishing process. Thus, as soon as the paper comes out, the data are automatically added to GBIF.

While BLR is expected to open up millions of scientific illustrations and descriptions, the system is unique in that it makes all the extracted data findable, accessible, interoperable and reusable (FAIR), as well as open to anybody, anywhere, at any time. Most of all, its purpose is to create a novel way to access scientific literature.

To date, BLR has extracted ~350,000 taxonomic treatments and ~200,000 figures from over 38,000 publications. This includes the descriptions of 55,800 new species, 3,744 new genera, and 28 new families. BLR has contributed to the discovery of over 30% of the ~17,000 species described annually.

Prof. Lyubomir Penev, founder and CEO of Pensoft says,

“It is such a great satisfaction to see how the development process of the TaxPub standard, started by Plazi some 15 years ago and implemented as a routine publishing workflow at Pensoft’s journals in 2010, has now resulted in an entire infrastructure that allows automated extraction and distribution of biodiversity data from various journals across the globe. With the recent announcement from the Consortium of European Taxonomic Facilities (CETAF) that their European Journal of Taxonomy is joining the TaxPub club, we are even more confident that we are paving the right way to fully grasping the dimensions of the world’s biodiversity.”

Dr Donat Agosti, co-founder and president of Plazi, adds:

“Finally, information technology allows us to create a comprehensive, extended catalogue of life and bring to light this huge corpus of cultural and scientific heritage – the description of life on Earth – for everybody. The nature of taxonomic treatments as a network of citations and syntheses of what scientists have discovered about a species allows us to link distinct fields such as genomics and taxonomy to specimens in natural history museums.”

Dr Tim Smith, Head of Collaboration, Devices and Applications Group at CERN, comments:

“Moving the focus away from the papers, where concepts are communicated, to the concepts themselves is a hugely significant step. It enables BLR to offer a unique new interconnected view of the species of our world, where the taxonomic treatments, their provenance, histories and their illustrations are all linked, accessible and findable. This is inspirational for the digital liberation of other fields of study!”


Additional information:

BLR is a joint project led by Plazi in partnership with Pensoft and Zenodo at CERN.

Currently, BLR is supported by a grant from Arcadia, a charitable fund of Lisbet Rausing and Peter Baldwin.

CASE STUDY: Data audit for the “Vascular plants dataset of the COFC herbarium (University of Cordoba, Spain)”, a data paper in PhytoKeys

Following the submission of their data paper manuscript, which serves to describe the herbarium dataset of vascular plants at the University of Cordoba (Spain), to the open access journal PhytoKeys, Dr Gloria Martínez-Sagarra and Prof Juan Antonio Devesa received a data audit report, prepared by data specialist Dr Robert Mesibov

The dataset described in Dr Gloria Martínez-Sagarra’s and Prof Juan Antonio Devesa’s paper is registered and available from the GBIF portal.

As part of the routine workflow, which is mandatory for data papers submitted across relevant Pensoft journals, their work underwent a technical evaluation against a checklist of data quality features, compiled in such a fashion that it ensures uncompromised accessibility, readability and interoperability of the data, regardless of whether its next user is a human or a machine. 

To do so, it is crucial that any issues concerning the data structure and format within a dataset – which could potentially cause data loss down the line – need to be identified and addressed prior to the publication of the data paper, in fact, before it is even assigned to a subject editor. Only after the data audit is performed, can a manuscript proceed to peer review. In case there are major issues with the dataset, the data paper can be rejected right away, but resubmitted after the necessary corrections are applied.

In the report, the authors could find a list of identified issues as well as recommendations from Dr Mesibov. Similarly to a conventional peer review, these comments are meant to pinpoint any areas that need to be corrected straight away, as well as those that might only need a bit of further clarification. After receiving the data audit report, the authors take their turn to address the feedback.

Snapshot from the data auditing report received by Dr Gloria Martínez-Sagarra and Prof Juan Antonio Devesa for their data paper manuscript submitted to PhytoKeys.

In the present case, the report features a list of discrepancies between the counts of taxonomic records as listed in the data paper as opposed to those in the original dataset, i.e. verbatim.txt. Here, as it turned out, the disagreement is due to various taxonomic revisions that have taken place within the highlighted families since the dataset’s last update on GBIF.

Dr Gloria Martínez-Sagarra and Prof Juan Antonio Devesa sent back their comments on the issues addressed in the data audit report.

In other cases, however, data entry errors, such as inappropriately used fields and  non-compliance with the Darwin Core recommendations, had to be cleaned, in order to prevent data loss and compromised interoperability.

With the problematic data corrected, the manuscript proceeded to peer review and was accepted for publication five days later.

Editor’s user interface on the PhytoKeys website showing the progress of the manuscript from submission to acceptance.

Having followed the strong recommendations from Pensoft, the authors also re-uploaded their revised data to GBIF.

Data audit workflow provided for data papers submitted to Pensoft journals.

As a result, both the data paper and the associated dataset are not only published in an open access, peer-reviewed journal and safely stored at GBIF, but also verified as Findable, Accessible, Interoperable and Reusable. 

Thanks to the thorough work and additional efforts of University of Cordoba’s Dr Gloria Martínez-Sagarra and Prof Juan Antonio Devesa, future researchers working on the Andalusian flora can already rely on a real head start.

Find more about the Pensoft’s mandatory data quality workflow in this blog post.