Category: Phytokeys

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 150^th 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 150^th 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.

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.
https://doi.org/10.3897/phytokeys.139.48717

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 ofPlazi, Pensoft 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.

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.

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.”

###

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.

Follow PhytoKeys on Twitter and Facebook for live updates and news across Kingdom Plantae.

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.

###

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

FAIR biodiversity data in Pensoft journals thanks to a routine data auditing workflow

To avoid publication of openly accessible, yet unusable datasets, fated to result in irreproducible and inoperable biological diversity research at some point down the road, Pensoft takes care for auditing data described in data paper manuscripts upon their submission to applicable journals in the publisher’s portfolio, including Biodiversity Data Journal, ZooKeys, PhytoKeys, MycoKeys and many others.

Once the dataset is clean and the paper is published, biodiversity data, such as taxa, occurrence records, observations, specimens and related information, become FAIR (findable, accessible, interoperable and reusable), so that they can be merged, reformatted and incorporated into novel and visionary projects, regardless of whether they are accessed by a human researcher or a data-mining computation.

As part of the pre-review technical evaluation of a data paper submitted to a Pensoft journal, the associated datasets are subjected to data audit meant to identify any issues that could make the data inoperable. This check is conducted regardless of whether the dataset are provided as supplementary material within the data paper manuscript or linked from the Global Biodiversity Information Facility (GBIF) or another external repository. The features that undergo the audit can be found in a data quality checklist made available from the website of each journal alongside key recommendations for submitting authors.

Once the check is complete, the submitting author receives an audit report providing improvement recommendations, similarly to the commentaries he/she would receive following the peer review stage of the data paper. In case there are major issues with the dataset, the data paper can be rejected prior to assignment to a subject editor, but resubmitted after the necessary corrections are applied. At this step, authors who have already published their data via an external repository are also reminded to correct those accordingly.

“It all started back in 2010, when we joined forces with GBIF on a quite advanced idea in the domain of biodiversity: a data paper workflow as a means to recognise both the scientific value of rich metadata and the efforts of the the data collectors and curators. Together we figured that those data could be published most efficiently as citable academic papers,” says Pensoft’s founder and Managing director Prof. Lyubomir Penev.

“From there, with the kind help and support of Dr Robert Mesibov, the concept evolved into a data audit workflow, meant to ‘proofread’ the data in those data papers the way a copy editor would go through the text,” he adds.

“The data auditing we do is not a check on whether a scientific name is properly spelled, or a bibliographic reference is correct, or a locality has the correct latitude and longitude”, explains Dr Mesibov. “Instead, we aim to ensure that there are no broken or duplicated records, disagreements between fields, misuses of the Darwin Core recommendations, or any of the many technical issues, such as character encoding errors, that can be an obstacle to data processing.”

At Pensoft, the publication of openly accessible, easy to access, find, re-use and archive data is seen as a crucial responsibility of researchers aiming to deliver high-quality and viable scientific output intended to stand the test of time and serve the public good.

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

To explain how and why biodiversity data should be published in full compliance with the best (open) science practices, the team behind Pensoft and long-year collaborators published a guidelines paper, titled “Strategies and guidelines for scholarly publishing of biodiversity data” in the open science journal Research Ideas and Outcomes (RIO Journal).

Aloe sanguinalis, a new red Aloe from Somaliland

Aloe sanguinalis, or Somali Red Aloe, forms large, conspicuous clumps and has blood red sap. Its can easily be spotted from the road, but the species has only just been named and described in the open access journal PhytoKeys.

It remains a mystery how this beautiful and showy aloe species has remained undescribed by science for so long, but one of the theory is that the plant was ‘hiding in plain sight’ in an area not usually known for its high biological diversity.

The locals in the area have long known that the plants were different from other kinds of “Dacar”, (the Somali name for Aloes) in the region and were referring to them as “Dacar cas” or “Red aloe”.

Similarly, the scientific name for the new species – Aloe sanguinalis – is based on one of its most distinct characters, its bright red color, coming from the peculiar blood-red sap the plant produces. The leaves also become reddish as they mature.

The story of the formal recognition of “Dacar cas” or Aloe sanguinalis, however, began when Ahmed Awale, a leading Somaliland environmentalist, spotted the large, reddish clumps plants, while driving through the country on behalf of Candlelight, an NGO focused on the environment, education, and health.

Later on, when the plant came to the attention of Mary Barkworth, a botanist interested in building botanical capacity in Somaliland. After listening to Ahmed, the two of them began looking formally into the possibility that “Dacar cas” was, indeed, an undescribed species. They were soon convinced it was. After the initial excitement, the next step required demonstrating that “Dacar Cas” differs from all the other 600+ known species of Aloe. That step took longer, but finally it has been done.

Aloe sanguinalis, or Dakar Cas, together with Ahmed Awale.

“This news comes from a region which had experienced periods of conflict and instability, climate change effects and accelerated environmental degradation, whereby much of the people’s attention has been focused on promoting livelihoods and resilience. With this positive piece of information we hope that we inspire scientists to further explore the area,” explains Dr Barkworth.

The new species is currently known from only two locations, but it is hoped that naming and sharing pictures of it online will encourage discovery and documentation of additional locations. Images and locality information for new locations are welcome at faisaljama24@gmail.com or mary.barkworth@usu.edu.

Original Source:

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