All processes fit into a broad S-shaped envelope extending from the briefest to the most enduring biological events. For the first time, we have the first simple model that depicts the scope and scale of biology.
Arctic tern by Mark Stock, Schleswig-Holstein Wadden Sea National Park. License: CC BY-SA.
As biology is progressing into a digital age, it is creating new opportunities for discovery.
Increasingly, information from investigations into aspects of biology from ecology to molecular biology is available in a digital form. Older ‘legacy’ information is being digitized. Together, the digital information is accumulated in databases from which it can be harvested and examined with an increasing array of algorithmic and visualization tools.
From this trend has emerged a vision that, one day, we should be able to analyze any and all aspects of biology in this digital world.
However, before this can happen, there will need to be an infrastructure that gathers information from ALL sources, reshapes it as standardized data using universal metadata and ontologies, and made freely available for analysis.
That information also must make its way to trustworthy repositories to guarantee the permanent access to the data in a polished and fully suited for re-use state.
The first layer in the infrastructure is the one that gathers all old and new information, whether it be about the migrations of ocean mammals, the sequence of bases in ribosomal RNA, or the known locations of particular species of ciliated protozoa.
How many of these subdomains will be there?
To answer this, we need to have a sense of the scope and scale of biology.
With the Nature’s Envelope we have, for the first time, a simple model that depicts the scope and scale of biology. Presented as a rhetorical device by its author Dr David J. Patterson (University of Sydney, Australia), the Nature’s Envelope is described in a Forum Paper, published in the open-science journal Research Ideas and Outcomes(RIO).
This is achieved by compiling information about the processes conducted by all living organisms. The processes occur at all levels of organization, from sub-molecular transactions, such as those that underpin nervous impulses, to those within and among plants, animals, fungi, protists and prokaryotes. Further, they are also the actions and reactions of individuals and communities; but also the sum of the interactions that make up an ecosystem; and finally, the consequences of the biosphere as a whole system.
Nature’s Envelope, in green, includes all processes carried out by, involving, or the result of the activities of any and all organisms. The axes depict the duration of events and the sizes of participants using a log10 scale. Image by David J. Patterson. License: CC BY.
In the Nature’s Envelope, information on sizes of participants and durations of processes from all levels of organization are plotted on a grid. The grid uses a logarithmic (base 10) scale, which has about 21 orders of magnitude of size and 35 orders of magnitude of time. Information on processes ranging from the subatomic, through molecular, cellular, tissue, organismic, species, communities to ecosystems is assigned to the appropriate decadal blocks.
Examples include movements from the stepping motion of molecules like kinesin that move forward 8 nanometres in about 10 milliseconds; or the migrations of Arctic terns which follow routes of 30,000 km or more from Europe to Antarctica over 3 to 4 months.
The extremes of life processes are determined by the smallest and largest entities to participate, and the briefest and most enduring processes.
The briefest event to be included is the transfer of energy from a photon to a photosynthetic pigment as the photon passes through a chlorophyll molecule several nanometres in width at a speed of 300,000 km per second. That transaction is conducted in about 10-17 seconds. As it involves the smallest subatomic particles, it defines the lower left corner of the grid.
The most enduring is the process of evolution that has been progressing for almost 4 billion years. The influence of the latter has created the biosphere (the largest living object) and affects the gas content of the atmosphere. This process established the upper right extreme of the grid.
All biological processes fit into a broad S-shaped envelope that includes about half of the decadal blocks in the grid. The envelope drawn round the initial examples is Nature’s Envelope.
“Nature’s envelope will be a useful addition to many discussions, whether they deal with the infrastructure that will manage the digital age of biology, or provide the context for education on the diversity and range of processes that living systems engage in.
The version of Nature’s Envelopepublished in the RIO journal is seen as a first version, to be refined and enhanced through community participation,”
comments Patterson.
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Original source:
Patterson DJ (2022) The scope and scale of the life sciences (‘Nature’s envelope’). Research Ideas and Outcomes 8: e96132. https://doi.org/10.3897/rio.8.e96132
In 2018, NHM London’s digitisation team started a project to digitise non-type herbarium material from the legume family. A recent data paper in the Biodiversity Data Journal reports on the outcomes.
You can find the original blog post by the Natural History Museum of London, reposted here with minor edits.
Legumes are a group of plants that include soybeans, peas, chickpeas, peanuts and lentils. They are a significant source of protein, fibre, carbohydrates, and minerals in our diet and some, like the cowpea, are resistant to droughts.
The project’s outcomes were published in a data paper in the Biodiversity Data Journal. Within the project, the digitisation team aimed to collectively digitise non-type herbarium material from the legume family. This includes rosewood trees (Dalbergia), padauk trees (Pterocarpus) and the Phaseolinae subtribe that contains many of the beans cultivated for human and animal food.
Guinea, Ethiopia, Sudan, Kenya, Uganda, Tanzania, Mozambique, Malawi and Madagascar
Asian
Bangladesh, Myanmar, Nepal, New Guinea and India
Southern and Central American
Guatemala, Honduras, El Salvador, Nicaragua, Bolivia, Argentina and Brazil
ODA-listed Countries
The legume groups: Dalbergia, Pterocarpus and Phaseolinae,were chosen for digitisation to support the development of dry beans as a sustainable and resilient crop, and to aid conservation and sustainable use of rosewood and padauk trees. Some of these beans, especially cow pea and pigeon pea, are sustainable and resilient crops, as they can be grown in poor-quality soils and are drought stress resistant. This makes them particularly suitable for agricultural production where the growing of other crops would be difficult.
Digitally discoverable herbarium specimens can provide important information about the distribution of individual species, as well as highlighting which species occur naturally together.
While there have been collaborative efforts between herbaria in the past, these have tended to prioritise digitisation of type specimens: the example specimens for which a species is named.
Types are important to identification, but being individual specimens, they don’t offer insights into species distribution over time. By focusing on the non-types across the world and over the last 200 years, we have released a brand-new resource to the global scientific community.
Searching for beans
This collection was digitised by creating an inventory record for each specimen, attaching images of each herbarium sheet, and then transcribing more data and georeferencing the specimens, providing an accurate locality in space and time for their collection.
We originally had four months and three members of staff to digitise over 11,000 specimens. The Covid-19 lockdown was ironically rather lucky for this project as it enabled us to have more time to transcribe and georeference all of the records.
say the researchers behind the digitisation project.
Map showing breakdown of records by country.
“We were able to assign country-level data to 10,857 out of the total number of 11,222 records. We were also able to transcribe the collectors’ names from the majority of our specimen labels (10,879 out of 11,222). Only 770 out of the 2,226 individuals identified during this project collected their specimens in ODA listed countries. The highest contributors were: Richard Beddome (130 specimens), Charles Clarke (110), Hans Schlieben (98) and Nathaniel Wallich (79). The breakdown of records by ODA country can be seen in the chart below. “
Map showing breakdown of records by country and pie chart showing distribution by ODA listed countries.
From our data, we can see the peak decade of collection was the 1930s, with almost half (4,583 specimens or 49,43%) collected between 1900 and 1950 (Fig. 10).
This peak can be attributed to three of our most prolific collectors: Arthur Kerr, John Gossweiler and Georges Le Testu, all of whom were most active in the 1930s. The oldest specimen (BM013713473) was collected by Mark Catesby (1683-1749) in the Bahamas in 1726.
they explain.
An interesting, but perhaps unsurprising, finding is that our collection is strongly male-dominated.
There are only two women (Caroline Whitefoord and Ynes Mexia) in the list of our top 50 plant collectors and they are not close to the most prolific collectors.
We identified more women in the rest of our records, but their contribution is on average less than 25 specimens per person in the dataset consisting of more than 10,000 specimens. In contrast, the top five male collectors contributed 10% of our collection.
they continued
Releasing Rosewoods
Both the Pterocarpus and Dalbergia genera include species that are used as expensive good quality timber that is prone to illegal logging. Many species such as Pterocarpus tinctorius are also listed on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. By releasing this new resource of information on all these plants from three of the biggest herbaria in the world, we can share this datа with the people who are taking care of biodiversity in these countries. The data can be used to identify hotspots, where the tree is naturally growing and protect these areas. These data would also allow much closer attention to be paid to areas that could be targets for illegal logging activity.
Pterocarpus tinctorius is a species of padauk tree that is listed as endangered on the IUCN Red List.
Cowpea (Vigna unguiculata) is a food and animal feed crop grown in the semi-arid tropics.
The ODA-listed countries are economically impoverished and disproportionately prone to be disadvantaged with the changing climate whether from flood or drought or increase in temperature.
Using data to identify good, nutritious plant species that can be grown in such conditions can therefore benefit local communities, potentially reducing dependence on imports, aid and on less resilient crops.
the team adds in conclusion.
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This dataset is now openly available on the Museum’s Data Portal and a data paper about this work has been released in the Biodiversity Data Journal.
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Discovering a new species is always exciting, but so is finding one alive that everyone assumed had been lost to the passage of time. A small clam, previously known only from fossils, has recently been found living at Naples Point, just up the coast from UC Santa Barbara. The discovery appears in the journal ZooKeys.
“It’s not all that common to find alive a species first known from the fossil record, especially in a region as well-studied as Southern California,” said co-author Jeff Goddard, a research associate at UC Santa Barbara’s Marine Science Institute. “Ours doesn’t go back anywhere near as far as the famous Coelacanth or the deep-water mollusk Neopilina galatheae — representing an entire class of animals thought to have disappeared 400 million years ago — but it does go back to the time of all those wondrous animals captured by the La Brea Tar Pits.”
Jeff Goddard with students. Photo Credit: Courtesy Image
On an afternoon low tide in November 2018, Goddard was turning over rocks searching for nudibranch sea slugs at Naples Point, when a pair of small, translucent bivalves caught his eye. “Their shells were only 10 millimeters long,” he said. “But when they extended and started waving about a bright white-striped foot longer than their shell, I realized I had never seen this species before.” This surprised Goddard, who has spent decades in California’s intertidal habitats, including many years specifically at Naples Point. He immediately stopped what he was doing to take close-up photos of the intriguing animals.
“I was surprised and intrigued. This was something I’d never seen before.”
Paul Valentich-Scott
With quality images in hand, Goddard decided not to collect the animals, which appeared to be rare. After pinning down their taxonomic family, he sent the images to Paul Valentich-Scott, curator emeritus of malacology at the Santa Barbara Museum of Natural History. “I was surprised and intrigued,” Valentich-Scott recalled. “I know this family of bivalves (Galeommatidae) very well along the coast of the Americas. This was something I’d never seen before.”
He mentioned a few possibilities to Goddard, but said he’d need to see the animal in-person to make a proper assessment. So, Goddard returned to Naples Point to claim his clam. But after two hours combing just a few square meters, he still hadn’t caught sight of his prize. The species would continue to elude him many more times.
Nine trips later, in March 2019, and nearly ready to give up for good, Goddard turned over yet another rock and saw the needle in the haystack. A single specimen, next to a couple of small white nudibranchs and a large chiton. Valentich-Scott would get his specimen at last, and the pair could finally set to work on identification.
A dazzling play of colors highlights Southern California’s long lost clam. Photo Credit: Jeff Goddard
Valentich-Scott was even more surprised once he got his hands on the shell. He knew it belonged to a genus with one member in the Santa Barbara region, but this shell didn’t match any of them. It raised the exciting possibility that they had found a new species.
“This really started ‘the hunt’ for me,” Valentich-Scott said. “When I suspect something is a new species, I need to track back through all of the scientific literature from 1758 to the present. It can be a daunting task, but with experience it can go pretty quickly.”
The two researchers decided to check out an intriguing reference to a fossil species. They tracked down illustrations of the bivalve Borniacooki from the paper describing the species in 1937. It appeared to match the modern specimen. If confirmed, this would mean that Goddard had found not a new species, but a sort of living fossil.
Cymatioa cooki. Photo credit: VALENTICH-SCOTT ET AL.
It is worth noting that the scientist who described the species, George Willett, estimated he had excavated and examined perhaps 1 million fossil specimens from the same location, the Baldwin Hills in Los Angeles. That said, he never found B. cooki himself. Rather, he named it after Edna Cook, a Baldwin Hills collector who had found the only two specimens known.
Valentich-Scott requested Willett’s original specimen (now classified as Cymatioacooki) from the Natural History Museum of Los Angeles County. This object, called the “type specimen,” serves to define the species, so it’s the ultimate arbiter of the clam’s identification.
The type specimen that George Willett used to originally describe the species. Photo credit: VALENTICH-SCOTT ET AL.
Meanwhile, Goddard found another specimen at Naples Point — a single empty shell in the sand underneath a boulder. After carefully comparing the specimens from Naples Point with Willett’s fossil, Valentich-Scott concluded they were the same species. “It was pretty remarkable,” he recalled.
Small size and cryptic habitat notwithstanding, all of this begs the question of how the clam eluded detection for so long. “There is such a long history of shell-collecting and malacology in Southern California — including folks interested in the harder to find micro-mollusks — that it’s hard to believe no one found even the shells of our little cutie,” Goddard said.
He suspects the clams may have arrived here on currents as planktonic larvae, carried up from the south during marine heatwaves from 2014 through 2016. These enabled many marine species to extend their distributions northward, including several documented specifically at Naples Point. Depending on the animal’s growth rate and longevity, this could explain why no one had noticed C. cooki at the site prior to 2018, including Goddard, who has worked on nudibranchs at Naples Point since 2002.
“The Pacific coast of Baja California has broad intertidal boulder fields that stretch literally for miles,” Goddard said, “and I suspect that down there Cymatioa cooki is probably living in close association with animals burrowing beneath those boulders.”
Research article:
Valentich-Scott P, Goddard JHR (2022) A fossil species found living off southern California, with notes on the genus Cymatioa (Mollusca, Bivalvia, Galeommatoidea). ZooKeys 1128: 53-62. https://doi.org/10.3897/zookeys.1128.95139
The invasive spotted wing drosophila (SWD), introduced from South-East Asia, is a well-known fruit crop pest. It lays its eggs by destroying the mechanical protection of the fruit’s skin, providing an entry point for further infestation. Egg deposition and inoculated microbes then accelerate decay, and as a result the fruit rots and becomes inedible. While this small fly is known to cause massive economic damage in agriculture, little is known about its ecological impact on more natural ecosystems such as forests.
The larvae of the invasive spotted wing drosophila develops in fruits of many forest species such as brambles. Its occurrence result in a fast decay of the fruits.
The research team assessed the use of potential host plants at 64 sites in forests from mid-June to mid-October 2020 by checking a total of 12,000 fruits for SWD egg deposits. To determine if SWD attacks trigger fruit decay, they also recorded symptoms of fruit decay after egg deposition. In addition, they monitored the fruit fly (drosophilid) fauna in the area, assuming that the SWD would outnumber and possibly outcompete other fruit-eating insects.
The male of the invasive spotted wing drosophila can be easily identified by the dark spots on the wings.
The authors found egg deposits on the fruits of 31 of the 39 fruit-bearing forest plant species they studied, with 18 species showing an attack rate of more than 50%. Furthermore, more than 50% of the affected plant species showed severe symptoms of decay after egg deposition. The egg depositions may alter the attractiveness of fruits, because they change their chemical composition and visual cues, such as colour, shape and reflective patterns, which in turn might lead seed dispersers such as birds to consume less fruits.
Given the large number of infested fruits, significant ecological impacts can be expected. “Rapid decay of fruits attacked by the spotted wing drosophila results in a loss of fruit available for other species competing for this resource, and may disrupt seed-dispersal mutualisms due to reduced consumption of fruit by dispersers such as birds,” says Prof. Martin M. Gossner, entomologist at the WSL. “If the fly reproduces in large numbers, both seed dispersers and plants could suffer.”
The females of the invasive spotted wing drosophila has an enlarged, serrated ovipositor to attack undamaged fruits, which gives it a competitive advantage over native fruit flies.
The authors further found that SWD were strongly represented and dominant in trap catches, and showed that the more abundant SWD were, the less abundant native drosophilids were. This suggests additional negative impacts of the invasive species on native communities.
With ongoing climate change, these potentially severe ecological impacts might be amplified in temperate forests, as higher average and winter temperatures will most likely lead to shorter generation times and lower winter mortality, which will eventually further increase the pressure on forest fruits and the competitiveness of the SWD over native drosophilids, the authors note.
Research article: Bühlmann I, Gossner MM (2022) Invasive Drosophila suzukii outnumbers native controphics and causes substantial damage to fruits of forest plants. NeoBiota 77: 39-77. https://doi.org/10.3897/neobiota.77.87319
A random survey in a poorly explored region of the southern Benguela Province of Angola, led to the discovery of a unique new spiny-tailed leaf-toed gecko.
After the long, hard days of fieldwork in the arid coastal region of southern Angola, Angolan researcher Pedro Vaz Pinto and his enthusiastic son Afonso, found the best spot to spend the night before heading back home. In the area of Carivo, every night was different: after four visits to this unique place, a different gecko species always showed up to add to the growing species list.
On a random night in August 2021, they went for a routine night walks and came across this unique gecko. In shock, Pedro immediately started sharing photos with the coauthors, Werner and Javier. “Guys, I think I found a new Kolekanos” he said.
Kolekanos is a unique and iconic gecko genus in Africa and more specifically only known from southwestern Angola. Kolekanos plumicaudus was described by one of the most recognized herpetologists in Africa, the late Wulf Haacke (1936– 2021).
Feather-tailed Kolekanos was at that point a monotypic genus (only one species in the genus), known only from ~200km south of the new discovery. Immediately, we all knew that what we were looking in that photo was something different from the known K. plumicaudus. “It is a Kolekanos… but, those are spines in the tail, not feathers…” was one of the most common reactions that night. So, we started planning our next trip to the area.
Three months later we were back at Carivo, now focusing on finding more specimens of that unique gecko. After only one hour, we spotted at least six specimens among the semi-dessert vegetations and rocks. At that moment, all doubt went away. The behavior and habitat of the new gecko was completely distinctive in comparison with K. plumicaudus.
Then, with our goal achieved and based on the big success of the first night, we planned to go back through different areas to explore some of the most remote regions in Northern Namibe and southern Benguela provinces. After two days driving on impossible roads, the team reached Ekongo. That night we were tired, so we decided to have a short walk around the camp. And… there it was…! Like a ghost, this small, cryptic, and elusive gecko started showing up in every big rock boulder.
This study, now published in the journal ZooKeys, also highlights how poorly explored and understood some regions of Angola remain, even as it has been considered as an important source of diversification and endemism in West Africa.
A new native bee species with a dog-like “snout” has been discovered in Perth bushland though Curtin-led research that sheds new light on our most important pollinators.
Published in the Journal of Hymenoptera Research, author Dr Kit Prendergast, from the Curtin School of Molecular and Life Sciences, has named the new species after her pet dog Zephyr after noticing a protruding part of the insect’s face looked similar to a dog’s snout, and to acknowledge the role her dog played in providing emotional support during her PhD.
Dr Prendergast said the rare and remarkable finding would add to existing knowledge about our evolving biodiversity and ensure the bees, named Leioproctus zephyr, were protected by conservation efforts.
“When I first examined the specimens that I collected during my PhD surveys discovering the biodiversity of native bees in urbanised regions of the southwest WA biodiversity hotspot, I was instantly intrigued by the bee’s very unusual face,” Dr Prendergast said.
Insects in general are so diverse and so important, yet we don’t have scientific descriptions or names for so many of them.
Dr Kit Prendergast
“When I went to identify it, I found it matched no described species, and I was sure that if it was a known species, it would be quite easy to identify given how unusual it was in appearance.
“You can only confirm a particular species once you look at them under a microscope and go through the long process of trying to match their characteristics against other identified species, then going through museum collections.
“When perusing the WA Museum’s Entomology collection, I discovered that a few specimens of Leioproctus zephyrus had first been collected in 1979, but it had never been scientifically described.”
Dr Prendergast said she was excited to play a role in making this species known and officially naming them.
“Insects in general are so diverse and so important, yet we don’t have scientific descriptions or names for so many of them,” Dr Prendergast said.
“The Leioproctus zephyr has a highly restricted distribution, only occurring in seven locations across the southwest WA to date, and have not been collected from their original location. They were entirely absent from residential gardens and only present at five urban bushland remnants that I surveyed, where they foraged on two plant species of Jacksonia.
“Not only is this species fussy, they also have a clypeus that looks like a snout. Hence, I named them after my dog Zephyr. She has been so important to my mental health and wellbeing during the challenging period of doing a PhD and beyond.”
Through DNA barcoding, Dr Prendergast was able to confirm that the new species was most closely related to other species of unidentified Leioproctus.
The Principe Scops-Owl, the eighth known bird species endemic to the island, has a unique call and lives in a restricted range in the Príncipe Obô Natural Park.
A new species of owl has just been described from Príncipe Island, part of the Democratic Republic of São Tomé and Príncipe in Central Africa. Scientists were first able to confirm its presence in 2016, although suspicions of its occurrence gained traction from 1998, and testimonies from local people suggesting its existence could be traced back as far as 1928.
Otus bikegila. Photo by Martim Melo
The new owl species was described in the open-access journal ZooKeys based on multiple lines of evidence such as morphology, plumage colour and pattern, vocalisations, and genetics. Data was gathered and processed by an international team led by Martim Melo (CIBIO and Natural History and Science Museum of the University of Porto), Bárbara Freitas (CIBIO and the Spanish National Museum of Natural Sciences) and Angelica Crottini (CIBIO).
Bárbara Freitas, Bikegila and Martim Melo pose with an owl. Photo by Martim Melo
The bird is now officially known as the Principe Scops-Owl, or Otus bikegila.
“Otus” is the generic name given to a group of small owls sharing a common history, commonly called scops-owls. They are found across Eurasia and Africa and include such widespread species as the Eurasian Scops-Owl (Otus scops) and the African Scops-Owl (Otus senegalensis).
Bikegila. Photo by Martim Melo
The scientists behind the discovery further explain that the species epithet “bikegila” was chosen in homage of Ceciliano do Bom Jesus, nicknamed Bikegila – a former parrot harvester from Príncipe Island and now a ranger of its natural park.
“The discovery of the Principe Scops-Owl was only possible thanks to the local knowledge shared by Bikegila and by his unflinching efforts to solve this long-time mystery,” the researchers say. “As such, the name is also meant as an acknowledgment to all locally-based field assistants who are crucial in advancing the knowledge on the biodiversity of the world.”
Martim Melo and Bikegila. Photo by Alexandre Vaz
In the wild, the easiest way to recognise one would be its unique call – in fact, it was one of the main clues leading to its discovery.
“Otus bikegila‘s unique call is a short “tuu” note repeated at a fast rate of about one note per second, reminiscent of insect calls. It is often emitted in duets, almost as soon as the night has fallen,” Martim Melo explains.
Otus bikegila’s call. Recording by Martim Melo
The entire Principe Island was extensively surveyed to determine the distribution and population size of the new species. Results, published in the journal Bird Conservation International, show that the Principe Scops-Owl is found only in the remaining old-growth native forest of Príncipe in the uninhabited southern part of the island. There, it occupies an area of about 15 km2, apparently due to a preference for lower elevations. In this small area (about four times the size of Central Park), the densities of the owl are relatively high, with the population estimated at around 1000-1500 individuals.
The difficult terrain of the uninhabited southern forests of Príncipe Island, home to the Príncipe Scops-Owl, was somewhat immortalised by José Correia, Portuguese collector for the American Museum of Natural History, when collecting there in 1928. He wrote in his diary: “I have been in very bad fields ready, but this is bad among the bad or worse among the worse”. Photo by Alexandre Vaz
Nevertheless, because all individuals of the species occur in this single and very small location (of which a part will be affected in the near future by the construction of a small hydro-electric dam), researchers have proposed that the species should be classified as ‘Critically Endangered’, the highest threat level on the IUCN Red List. This recommendation must still be evaluated by the International Union for Conservation of Nature.
Otus Bikegila. Photo by Martim Melo
Monitoring the population will be essential to get more precise estimates of its size and follow its trends. For this purpose, a survey protocol relying on the deployment of automatic recording units and AI to retrieve the data from these has been designed and successfully tested.
“The discovery of a new species that is immediately evaluated as highly threatened illustrates well the current biodiversity predicament”, the researchers say. “On a positive note, the area of occurrence of the Principe Scops-Owl is fully included within the Príncipe Obô Natural Park, which will hopefully help secure its protection.”
A view of the owl’s habitat. Photo by Martim Melo
Thisis the eighth known species of bird endemic to Príncipe, further highlighting the unusually high level of bird endemism for this island of only 139 km2.
Otus Bikegila. Photo by Paul van Giersbergen
Even though a new species of scops-owl was just described from Príncipe, genetic data indicated that the island was, surprisingly, likely the first in the Gulf of Guinea to be colonised by a species of scops-owl.
“Although it may seem odd for a bird species to remain undiscovered for science for so long on such a small island, this is by no means an isolated case when it comes to owls,” the researchers state. “For example, the Anjouan Scops-Owl was rediscovered in 1992, 106 years after its last observation, on Anjouan Island (also known as Ndzuani) in the Comoro Archipelago, and the Flores Scops-Owl was rediscovered in 1994, 98 years after the previous report.”
“The discovery of a new bird species is always an occasion to celebrate and an opportunity to reach out to the general public on the subject of biodiversity,” says Martim Melo. “In this age of human-driven extinction, a major global effort should be undertaken to document what may soon not be anymore,” he and his team state in their paper.
Otus bikegila. Photo by Philippe Verbelen
“Birds are likely the best studied animal group. As such, the discovery of a new bird species in the 21st century underscores both the actuality of field-based explorations aiming at describing biodiversity, and how such curiosity-driven endeavour is more likely to succeed when coupled with local ecological knowledge, the participation of keen amateur naturalists, and persistence,” they add.
They believe that this “new wave of exploration, carried out by professionals and amateurs alike”, will help rekindle the link to the natural world, which will be essential to help revert the global biodiversity crisis.
Research article:
Melo M, Freitas B, Verbelen P, da Costa SR, Pereira H, Fuchs J, Sangster G, Correia MN, de Lima RF, Crottini A (2022) A new species of scops-owl (Aves, Strigiformes, Strigidae, Otus) from Príncipe Island (Gulf of Guinea, Africa) and novel insights into the systematic affinities within Otus. ZooKeys 1126: 1-54. https://doi.org/10.3897/zookeys.1126.87635
Key figures from Naturalis Biodiversity Center, Plazi and Pensoft were amongst the first to sign the Declaration at the closing session of the First International Conference on FAIR Digital Objects (FDO2022)
Several of the BiCIKL partners signed the Leiden Declaration on FAIR Digital Objects, thereby committing to “a new environment that works as a truly meaningful data space,” as framed by the organisers of the conference, whose first instalment turned out to be the perfect occasion for the formal publication of the pact.
The conference brought together key international technical, scientific, industry and science-policy stakeholders with the aim to boost the development and implementation of FAIR Digital Objects (FDOs) worldwide. It was organised by the FDO Forum, an initiative supported by major global initiatives and by a variety of regional and national initiatives with the shared goal to achieve a better coherence amongst the increasing number of initiatives working on FDO-based designs and implementations.
By joining the Declaration’s signees, the BiCIKL partners formally committed to:
Support the FAIR guiding principles to be applied (ultimately) to each digital object in a web of FAIR data and services;
Support open standards and protocols;
Support data and services to be as open as possible, and only as restricted as necessary;
Support distributed solutions where useful to achieve robustness and scalability, but recognise the need for centralised approaches where necessary;
Support the restriction of standards and protocols to the absolute minimum;
Support freedom to operate wherever possible;
Help to avoid monopolies and provider lock-in wherever possible.
During the event, Plazi and Pensoft held a presentation demonstrating how their Biodiversity Literature Repository turns taxonomic treatments ‘locked’ in legacy scientific literature into FAIR Digital Objects. As a result of the collaboration between Plazi and Pensoft – a partnership long-preceding their involvement in BiCIKL – this workflow has also been adapted to modern-day publishing, in order to FAIRify data as soon as it is published.
A slide from the Plazi presentation at the FDO2022, Leiden, the Netherlands. Credit: Plazi.
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Ahead of FDO2022, all submitted conference abstracts – including the one associated with Plazi’s presentation – were made publicly available in a collection of their own in Pensoft’s open-science journal Research Ideas and Outcomes (RIO). Thus, not only did the organisers make the conference outputs available to the participants early on, so that they can familiarise themselves with the upcoming talks and topics in advance, but they also ensure that the contributions are permanently preserved and FAIR in their own turn.
The conference collection, guest edited by Tina Loo (Naturalis Biodiversity Center), contains a total of 51 conference abstracts, where each is published in HTML, XML and PDF formats, and assigned with its own persistent identifier (DOI) just like the collection in its entirety (10.3897/rio.coll.190).
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Read more about the declaration and sign it yourself from this link. You can also follow the FDO Forum on Twitter (@FAIRDOForum).
The FAIR Data Place – the key and final product of the partnership – is meant to provide scientists with all types of biodiversity data “at their fingertips”
The Horizon 2020 – funded project BiCIKL has reached its halfway stage and the partners gathered in Plovdiv (Bulgaria) from the 22nd to the 25th of October for the Second General Assembly, organised by Pensoft.
The BiCIKL project will launch a new European community of key research infrastructures, researchers, citizen scientists and other stakeholders in the biodiversity and life sciences based on open science practices through access to data, tools and services.
BiCIKL’s goal is to create a centralised place to connect all key biodiversity data by interlinking 15 research infrastructures and their databases. The 3-year European Commission-supported initiative kicked off in 2021 and involves 14 key natural history institutions from 10 European countries.
BiCIKL is keeping pace as expected with 16 out of the 48 final deliverables already submitted, another 9 currently in progress/under review and due in a few days. Meanwhile, 21 out of the 48 milestones have been successfully achieved.
Prof. Lyubomir Penev (BiCIKL’s project coordinator Prof. Lyubomir Penev and CEO and founder of Pensoft) opens the 2nd General Assembly of BiCIKL in Plovdiv, Bulgaria.
The hybrid format of the meeting enabled a wider range of participants, which resulted in robust discussions on the next steps of the project, such as the implementation of additional technical features of the FAIR Data Place (FAIR being an abbreviation for Findable, Accessible, Interoperable and Reusable).
This FAIR Data Place online platform – the key and final product of the partnership and the BiCIKL initiative – is meant to provide scientists with all types of biodiversity data “at their fingertips”.
This data includes biodiversity information, such as detailed images, DNA, physiology and past studies concerning a specific species and its ‘relatives’, to name a few. Currently, the issue is that all those types of biodiversity data have so far been scattered across various databases, which in turn have been missing meaningful and efficient interconnectedness.
Additionally, the FAIR Data Place, developed within the BiCIKL project, is to give researchers access to plenty of training modules to guide them through the different services.
Halfway through the duration of BiCIKL, the project is at a turning point, where crucial discussions between the partners are playing a central role in the refinement of the FAIR Data Place design. Most importantly, they are tasked with ensuring that their technologies work efficiently with each other, in order to seamlessly exchange, update and share the biodiversity data every one of them is collecting and taking care of.
By Year 3 of the BiCIKL project, the partners agree, when those infrastructures and databases become efficiently interconnected to each other, scientists studying the Earth’s biodiversity across the world will be in a much better position to build on existing research and improve the way and the pace at which nature is being explored and understood. At the end of the day, knowledge is the stepping stone for the preservation of biodiversity and humankind itself.
The Biodiversity Knowledge Hub is no longer existing on paper only! We are opening the 2nd day of the #BiCIKL_H2020 General Assembly looking at the prototype of the BKH created by the @LifeWatchERIC team. It's so exciting to see projects taking shape! 🤩 #Plovdivpic.twitter.com/RidzwBpxZx
“Needless to say, it’s an honour and a pleasure to be the coordinator of such an amazing team spanning as many as 14 partnering natural history and biodiversity research institutions from across Europe, but also involving many global long-year collaborators and their infrastructures, such as Wikidata, GBIF, TDWG, Catalogue of Life to name a few,”
said BiCIKL’s project coordinator Prof. Lyubomir Penev, CEO and founder of Pensoft.
“I see our meeting in Plovdiv as a practical demonstration of our eagerness and commitment to tackle the long-standing and technically complex challenge of breaking down the silos in the biodiversity data domain. It is time to start building freeways between all biodiversity data, across (digital) space, time and data types. After the last three days that we spent together in inspirational and productive discussions, I am as confident as ever that we are close to providing scientists with much more straightforward routes to not only generate more biodiversity data, but also build on the already existing knowledge to form new hypotheses and information ready to use by decision- and policy-makers. One cannot stress enough how important the role of biodiversity data is in preserving life on Earth. These data are indeed the groundwork for all that we know about the natural world”
Prof. Lyubomir Penev added.
Christos Arvanitidis (CEO of LifeWatch ERIC) at the 2nd General Assembly of the BiCIKL project.
“The point is: do we want an integrated structure or do we prefer federated structures? What are the pros and cons of the two options? It’s essential to keep the community united and allied because we can’t afford any information loss and the stakeholders should feel at home with the Project and the Biodiversity Knowledge Hub.”
Joe Miller, Executive Secretary and Director at GBIF, commented:
“We are a brand new community, and we are in the middle of the growth process. We would like to already have answers, but it’s good to have this kind of robust discussion to build on a good basis. We must find the best solution to have linkages between infrastructures and be able to maintain them in the future because the Biodiversity Knowledge Hub is the location to gather the community around best practices, data and guidelines on how to use the BiCIKL services… In order to engage even more partners to fill the eventual gaps in our knowledge.”
Joana Pauperio (biodiversity curator at EMBL-EBI) atthe 2nd General Assembly of the BiCIKL project.
“BiCIKL is leading data infrastructure communities through some exciting and important developments”
said Dr Guy Cochrane, Team Leader for Data Coordination and Archiving and Head of the European Nucleotide Archive at EMBL’s European Bioinformatics Institute (EMBL-EBI).
“In an era of biodiversity change and loss, leveraging scientific data fully will allow the world to catalogue what we have now, to track and understand how things are changing and to build the tools that we will use to conserve or remediate. The challenge is that the data come from many streams – molecular biology, taxonomy, natural history collections, biodiversity observation – that need to be connected and intersected to allow scientists and others to ask real questions about the data. In its first year, BiCIKL has made some key advances to rise to this challenge,”
“As a partner, we, at the Biodiversity Information Standards – TDWG, are very enthusiastic that our standards are implemented in BiCIKL and serve to link biodiversity data. We know that joining forces and working together is crucial to building efficient infrastructures and sharing knowledge.”
The project will go on with the first Round Table of experts in December and the publications of the projects who participated in the Open Call and will be founded at the beginning of the next year.
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Learn more about BiCIKL on the project’s website at: bicikl-project.eu
For the 37th time, experts from across the world to share and discuss the latest developments surrounding biodiversity data and how they are being gathered, used, shared and integrated across time, space and disciplines.
Between 17th and 21st October, about 400 scientists and experts took part in a hybrid meeting dedicated to the development, use and maintenance of biodiversity data, technologies, and standards across the world.
For the 37th time, the global scientific and educational association Biodiversity Information Standards (TDWG) brought together experts from all over the globe to share and discuss the latest developments surrounding biodiversity data and how they are being gathered, used, shared and integrated across time, space and disciplines.
This was the first time the event happened in a hybrid format. It was attended by 160 people on-site, while another 235 people joined online.
The TDWG 2022 conference saw plenty of networking and engaging discussions with as many as 160 on-site attendees and another 235 people, who joined the event remotely.
“It’s wonderful to be in the Balkans and Bulgaria for our Biodiversity Information and Standards (TDWG) 2022 conference! Everyone’s been so welcoming and thoughtfully engaged in conversations about biodiversity information and how we can all collaborate, contribute and benefit,”
“Our TDWG mission is to create, maintain and promote the use of open, community-driven standards to enable sharing and use of biodiversity data for all,”
she added.
Prof Lyubomir Penev (Pensoft) and Deborah Paul (TDWG) at TDWG 2022.
“We are proud to have been selected to be the hosts of this year’s TDWG annual conference and are definitely happy to have joined and observed so many active experts network and share their know-how and future plans with each other, so that they can collaborate and make further progress in the way scientists and informaticians work with biodiversity information,”
said Pensoft’s founder and CEO Prof. Lyubomir Penev.
“As a publisher of multiple globally renowned scientific journals and books in the field of biodiversity and ecology, at Pensoft we assume it to be our responsibility to be amongst the first to implement those standards and good practices, and serve as an example in the scholarly publishing world. Let me remind you that it is the scientific publications that present the most reliable knowledge the world and science has, due to the scrutiny and rigour in the review process they undergo before seeing the light of day,”
he added.
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In a nutshell, the main task and dedication of the TDWG association is to develop and maintain standards and data-sharing protocols that support the infrastructures (e.g., The Global Biodiversity Information Facility – GBIF), which aggregate and facilitate use of these data, in order to inform and expand humanity’s knowledge about life on Earth.
It is the goal of everyone at TDWG to let scientists interested in the world’s biodiversity to do their work efficiently and in a manner that can be understood, shared and reused.
It is the goal of everyone volunteering their time and expertise to TDWG to enable the scientists interested in the world’s biodiversity to do their work efficiently and in a manner that can be understood, shared and reused by others. After all, biodiversity data underlie everything we know about the natural world.
If there are optimised and universal standards in the way researchers store and disseminate biodiversity data, all those biodiversity scientists will be able to find, access and use the knowledge in their own work much more easily. As a result, they will be much better positioned to contribute new knowledge that will later be used in nature and ecosystem conservation by key decision-makers.
On Monday, the event opened with welcoming speeches by Deborah Paul and Prof. Lyubomir Penev in their roles of the Chair of TDWG and the main host of this year’s conference, respectively.
The opening ceremony continued with a keynote speech by Prof. Pavel Stoev, Director of the Natural History Museum of Sofia and co-host of TDWG 2022.
Prof. Pavel Stoev (Natural History Museum of Sofia) with a presentation about the known and unknown biodiversity of Bulgaria during the opening plenary session of TDWG 2022.
He walked the participants through the fascinating biodiversity of Bulgaria, but also the worrying trends in the country associated with declining taxonomic expertise.
He finished his talk with a beam of hope by sharing about the recently established national unit of DiSSCo, whose aim – even if a tad too optimistic – is to digitise one million natural history items in four years, of which 250,000 with photographs. So far, one year into the project, the Bulgarian team has managed to digitise more than 32,000 specimens and provide images to 10,000 specimens.
The plenary session concluded with a keynote presentation by renowned ichthyologist and biodiversity data manager Dr. Richard L. Pyle, who is also a manager of ZooBank – the key international database for newly described species.
Keynote presentation by Dr Richard L. Pyle (Bishop Museum, USA) at the opening plenary session of TDWG 2022.
In his talk, he highlighted the gaps in the ways taxonomy is being used, thereby impeding biodiversity research and cutting off a lot of opportunities for timely scientific progress.
“There are simple things we can do to change how we use taxonomy as a tool that would dramatically improve our ability to conduct science and understand biodiversity. There is enormous value and utility within existing databases around the world to understand biodiversity, how threatened it is, what impacts human activity has (especially climate change), and how to optimise the protection and preservation of biodiversity,”
he said in an interview for a joint interview by the Bulgarian News Agency and Pensoft.
“But we do not have easy access to much of this information because the different databases are not well integrated. Taxonomy offers us the best opportunity to connect this information together, to answer important questions about biodiversity that we have never been able to answer before. The reason meetings like this are so important is that they bring people together to discuss ways of using modern informatics to greatly increase the power of the data we already have, and prioritise how we fill the gaps in data that exist. Taxonomy, and especially taxonomic data integration, is a very important part of the solution.”
Pyle also commented on the work in progress at ZooBank ten years into the platform’s existence and its role in the next (fifth) edition of the International Code of Zoological Nomenclature, which is currently being developed by the International Commission of Zoological Nomenclature (ICZN).
“We already know that ZooBank will play a more important role in the next edition of the Code than it has for these past ten years, so this is exactly the right time to be planning new services for ZooBank. Improvements at ZooBank will include things like better user-interfaces on the web to make it easier and faster to use ZooBank, better data services to make it easier for publishers to add content to ZooBank as part of their publication workflow, additional information about nomenclature and taxonomy that will both support the next edition of the Code, and also help taxonomists get their jobs done more efficiently and effectively. Conferences like the TDWG one are critical for helping to define what the next version of ZooBank will look like, and what it will do.”
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During the week, the conference participants had the opportunity to enjoy a total of 140 presentations; as well as multiple social activities, including a field trip to Rila Monastery and a traditional Bulgarian dinner.
TDWG 2022 conference participants document their species observations on their way to Rila Monastery.
While going about the conference venue and field trip localities, the attendees were also actively uploading their species observations made during their stay in Bulgaria on iNaturalist in a TDWG2022-dedicated BioBlitz. The challenge concluded with a total of 635 observations and 228 successfully identified species.
Amongst the social activities going on during TDWG 2022 was a BioBlitz, where the conference participants could uploade their observations made in Bulgaria on iNaturalist and help each other successfully identify the specimens.
“Biodiversity provides the support systems for all life on Earth. Yet the natural world is in peril, and we face biodiversity and climate emergencies. The consequences of these include accelerating extinction, increased risk from zoonotic disease, degradation of natural capital, loss of sustainable livelihoods in many of the poorest yet most biodiverse countries of the world, challenges with food security, water scarcity and natural disasters, and the associated challenges of mass migration and social conflicts.
Solutions to these problems can be found in the data associated with natural science collections. DiSSCo is a partnership of the institutions that digitise their collections to harness their potential. By bringing them together in a distributed, interoperable research infrastructure, we are making them physically and digitally open, accessible, and usable for all forms of research and innovation.
At present rates, digitising all of the UK collection – which holds more than 130 million specimens collected from across the globe and is being taken care of by over 90 institutions – is likely to take many decades, but new technologies like machine learning and computer vision are dramatically reducing the time it will take, and we are presently exploring how robotics can be applied to accelerate our work.”
In his turn, Dr Donat Agosti, CEO and Managing director at Plazi – a not-for-profit organisation supporting and promoting the development of persistent and openly accessible digital taxonomic literature – said:
“All the data about biodiversity is in our libraries, that include over 500 million pages, and everyday new publications are being added. No person can read all this, but machines allow us to mine this huge, very rich source of data. We do not know how many species we know, because we cannot analyse with all the scientists in this library, nor can we follow new publications. Thus, we do not have the best possible information to explore and protect our biological environment.”
Dr Donat Agosti demonstrating the importance of publishing biodiversity data in a structured and semantically enhanced format in one of his presentations at TDWG 2022.
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At the closing plenary session, Gail Kampmeier – TDWG Executive member and one of the first zoologists to join TDWG in 1996 – joined via Zoom to walk the conference attendees through the 37-year history of the association, originally named the Taxonomic Databases Working Group, but later transformed to Biodiversity Information Standards, as it expanded its activities to the whole range of biodiversity data.
“While this presentation is about TDWG’s history as an organisation, its focus will be on the heart of TDWG: its people. We would like to show how the organisation has evolved in terms of gender balance, inclusivity actions, and our engagement to promote and enhance diversity at all levels. But more importantly, where do we—as a community—want to go in the future?”,
Then, in the final talk of the session, Deborah Paul took to the stage to present the progress and key achievements by the association from 2022.
🤩Year in review by @idbdeb at #TDWG2022: many wonderful achievements & even more in the works!🙌 E.g.✅Memorandum of Understanding with Genomic Standards Consortium ✅new Mineralogy Task Group ✅new vision & mission statement ✅collaboration with @GBIF on the new data model.. 1/ pic.twitter.com/RZx8hlePOm
Deborah Paul reminds that – apart from the conference abstracts – the TDWG journal: Biodiversity Information Science and Standards (BISS) also welcomes full-lenght articles that demonstrate the development or application of new methods and approaches in biodiversity informatics.
Launched in 2017 on the Pensoft’s publishing platform ARPHA, the journal provides the quite unique and innovative opportunity to have both abstracts and full-length research papers published in a modern, technologically-advanced scholarly journal. In her speech, Deborah Paul reminded that BISS journal welcomes research articles that demonstrate the development or application of new methods and approaches in biodiversity informatics in the form of case studies.
Amongst the achievements of TDWG and its community, a special place was reserved for the Horizon 2020-funded BiCIKL project (abbreviation for Biodiversity Community Integrated Knowledge Library), involving many of the association’s members.
Having started in 2021, the 3-year project, coordinated by Pensoft, brings together 14 partnering institutions from 10 countries, and 15 biodiversity under the common goal to create a centralised place to connect all key biodiversity data by interlinking a total of 15 research infrastructures and their databases.
Deborah Paul also reported on the progress of the Horizon 2020-funded project BiCIKL, which involves many of the TDWG members. BiCIKL’s goal is to create a centralised place to connect all key biodiversity data by interlinking 15 key research infrastructures and their databases.
In fact, following the week-long TDWG 2022 conference in Sofia, a good many of the participants set off straight for another Bulgarian city and another event hosted by Pensoft. The Second General Assembly of BiCIKL took place between 22nd and 24th October in Plovdiv.
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You can also explore highlights and live tweets from TDWG 2022 on Twitter via #TDWG2022.
The Pensoft team at TDWG 2022 were happy to become the hosts of the 37th TDWG conference.
