Diseases are among the major causes of tree mortality in both forests and urban areas. New diseases are continually being introduced, and pathogens are continually jumping to new hosts, threatening more and more tree species. When exposed to novel hosts, emerging diseases can cause mortality previously unseen in the native range.
Although not all diseases will outright kill their hosts, some can dramatically affect host populations. In the 20th century, chestnut blight, perhaps the most well-known tree disease in North America, effectively eliminated chestnut as an overstory tree in its native range in the Appalachian Mountains. More recently, we’ve seen sudden oak death in California, ash dieback in Europe, and butternut canker in the eastern US, each having the potential to eliminate host tree populations and alter the ecosystems where they occur.
“The continued emergence and accumulation of new diseases increases the likelihood of a particularly detrimental one emerging, and harming host tree populations,” says Dr Andrew Gougherty, research landscape ecologist at the USDA Forest Service. Recently, he has been exploring where tree diseases have accumulated fastest, and which trees are most impacted by new diseases. This information could help researchers and land managers better predict where new diseases may be most likely to emerge.
The study, recently published in the open-access journal NeoBiota, analyzes over 900 new disease reports on 284 tree species in 88 countries and quantified how emerging infectious diseases have accumulated geographically and on different hosts. “The ‘big data’ approach used in this study helps to characterise the growing threat posed by emergent infectious diseases and how this threat is unequally distributed regionally and by host species,” the author writes.
Dr Gougherty found that globally, the number of emerged diseases has accumulated rapidly over the past two decades. “The accumulation is apparent both where tree species are native and where they are not native, and the number of new disease emergences globally were found to double every ~11 years,” he explains. Among the trees he assessed, pines accumulated the most new diseases, followed by oaks and eucalypts. This, he explains, is likely due to their wide native distribution in the Northern Hemisphere, and the planting of pine forests throughout the globe. Europe, in aggregate, had the greatest total accumulation of new diseases, but North America and Asia were close behind.
In addition, he found more emerging tree diseases in areas where tree species were native versus non-native, with the exception of Latin America and the Caribbean, likely because most of the trees he assessed were not native to this region.
“Unfortunately, there is little evidence of saturation in emergent tree disease accumulation. Global trends show little sign of slowing, suggesting the impact of newly emerged diseases is likely to continue to compound and threaten tree populations globally and into the future,” warns Dr Gougherty. “Climate change is likely also playing a role, both by creating more favourable conditions for pathogens and by stressing host plants.”
Today, 16 September 2023, we are celebrating our tenth anniversary: an important milestone that has prompted us to reflect on the incredible journey thatBiodiversity Data Journal (BDJ) has been through.
From the very beginning, our mission was clear: to revolutionise the way biodiversity data is shared, accessed, and harnessed. This journey has been one of innovation, collaboration, and a relentless commitment to making biodiversity data FAIR – Findable, Accessible, Interoperable, and Reusable.
Over the past 10 years, BDJ, under the auspices of our esteemed publisher Pensoft, has emerged as a trailblazing force in biodiversity science. Our open-access platform has empowered researchers from around the world to publish comprehensive papers that seamlessly blend text with morphological descriptions, occurrences, data tables, and more. This holistic approach has enriched the depth of research articles and contributed to the creation of an interconnected web of biodiversity information.
In addition, by utilising ARPHA Writing Tool and ARPHA Platform as our entirely online manuscript authoring and submission interface, we have simplified the integration of structured data and narrative, reinforcing our commitment to simplifying the research process.
One of our most significant achievements is democratising access to biodiversity data. By dismantling access barriers, we have catalysed the emergence of novel research directions, equipping scientists with the tools to combat critical global challenges such as biodiversity loss, habitat degradation, and climate fluctuations.
We firmly believe that data should be openly accessible to all, fostering collaboration and accelerating scientific discovery. By upholding the FAIR principles, we ensure that the datasets accompanying our articles are not only discoverable and accessible, but also easy to integrate and reusable across diverse fields.
As we reflect on the past decade, we are invigorated by the boundless prospects on the horizon. We will continue working on to steer the global research community towards a future where biodiversity data is open, accessible, and harnessed to tackle global challenges.
Ten years of biodiversity research
To celebrate our anniversary, we have curated some of our most interesting and memorable BDJ studies from the past decade.
Recently, news outlets were quick to cover a new species of ‘snug’ published in our journal.
This Golden Retriever trained to monitor hermit beetle larvae proved once again the incredible capabilities of our canine friends.
Who could forget this tiny fly named after the former Governor of California?
Or this snail named after climate activist Greta Thunberg?
New discoveries are always exciting, but some of our favourite research focuses on formerly lost species, back where they belong.
Like the griffon vulture, successfully reintroduced to Bulgaria after fifty years.
Citizen science has shown time and time again that it holds an important position in biodiversity research.
This group, for example, who found a beetle the size of a pinhead in Borneo.
We extend our heartfelt gratitude to our authors, reviewers, readers, and the entire biodiversity science community for being integral parts of this transformative journey. Together, we have redefined scientific communication, and we will continue to push the boundaries of knowledge.
“In the present biodiversity crisis scenario, it is critical that we do not neglect basic scientific disciplines like taxonomy, since cataloguing biodiversity is a fundamental step towards its preservation.”
The knowledge of biodiversity in allegedly well-known places is not as complete as one would expect and its detailed study by researchers continues to offer surprises, is what we find out in a new study of the flora of south-central Spain.
Now, Spanish botanists from Pablo de Olavide University (Seville, Spain) have described a new plant species of the papyrus family (Cyperaceae) restricted to the La Mancha region in south-central Spain. This region is in fact well-known for classic literary fans, who might recognise the name as the main setting in Miguel de Cervantes’ (1547–1616) masterpiece Don Quixote.
The epic novel, which tells the story of the life and journeys of Alonso Quijano, a Spanish hidalgo (nobleman), who becomes the knight-errant Don Quixote de la Mancha, is commonly considered to be one of the greatest literary works ever written, with its number of editions and translations thought to be only surpassed by those of the Bible.
The new species, now scientifically known as Carex quixotiana, belongs to sedges of the genus Carex, a group of herbs included in the papyrus family (Cyperaceae). The classification (taxonomy) of these plants is difficult, as it is a highly diverse and widely distributed genus, whose species are frequently hard to tell apart. In fact, C. quixotiana has itself evaded the eyes of expert botanists for decades, because of its close resemblance to related species.
“Cryptic species are frequent in complex plant groups, such as sedges, and integrative studies encompassing different data sources (e.g. morphology, molecular phylogeny, chromosome number, ecological requirements) are needed to unravel systematic relationships and accurately describe biodiversity patterns,”
says Dr. Martín-Bravo, senior author of the paper.
After a preliminary genetic study pointed to something odd about specimens of what was later to be known as Carex quixotiana, the authors set off on exhaustive field collecting campaigns across La Mancha. As they studied additional populations of the plant in further detail, using morphology, phylogenetics, and chromosome number, the scientists confirmed that they were looking at a species previously unknown to science. Understandably, the distribution range of the newly discovered species, restricted to the mountain ranges surrounding La Mancha (Sierra Madrona and Montes de Toledo), made the authors think about Cervantes’ masterpiece.
So far only known from 16 populations, Carex quixotiana prefers habitats with high water availability, such as small streams, wet meadows and riverside (riparian) forests.
Since little is known about the species’ demographics, including the number of mature individuals in the wild, further investigation is required to determine its conservation status. However, based on what they have learnt so far about the species, the authors of the present study assume that:
In conclusion, the scientists point to their results as yet another proof of how much there is still to learn about Earth’s biodiversity, even when it comes to supposedly well-known organisms, such as flowering plants, and countries, whose flora is presumed to be fully documented. The “Flora Iberica”, for example, which covers Spain and Portugal, has only recently been finalised, the team reminds us.
Benítez-Benítez C, Jiménez-Mejías P, Luceño M, Martín-Bravo S (2023) Carex quixotiana (Cyperaceae), a new Iberian endemic from Don Quixote’s land (La Mancha, S Spain). PhytoKeys 221: 161-186. https://doi.org/10.3897/phytokeys.221.99234
EIVE 1.0 is the most comprehensive system of ecological indicator values of vascular plants in Europe to date. It can be used as an important tool for continental-scale analyses of vegetation and floristic data.
It took seven years and hundreds of hours of work by an international team of 34 authors to develop and publish the most comprehensive system of ecological indicator values (EIVs) of vascular plants in Europe to date.
EIVE 1.0 provides the five most-used ecological indicators, M – moisture, N – nitrogen, R – reaction, L – light and T – temperature, for a total of 14,835 vascular plant taxa in Europe, or between 13,748 and 14,714 for the individual indicators. For each of these taxa, EIVE contains three values: the EIVE niche position indicator, the EIVE niche width indicator and the number of regional EIV systems on which the assessment was based. Both niche position and niche width are given on a continuous scale from 0 to 10, not as categorical ordinal values as in the source systems.
Evidently, EIVE can be an important tool for continental-scale analyses of vegetation and floristic data in Europe.
It will allow to analyse the nearly 2 million vegetation plots currently contained in the European Vegetation Archive (EVA; Chytrý et al. 2016) in new ways.
Since EVA apart from elevation, slope inclination and aspect hardly contains any in situ measured environmental variables, the numerous macroecological studies up to date had to rely on coarse modelled environmental data (e.g. climate) instead. This is particularly problematic for soil variables such as pH, moisture or nutrients, which can change dramatically within a few metres.
Here, the approximation of site conditions by mean ecological indicator values can improve the predictive power substantially (Scherrer and Guisan 2019). Likewise, in broad-scale vegetation classification studies, mean EIVE values per plot would allow a better characterisation of the distinguished vegetation units. Lastly, one should not forget that most countries in Europe do not have a national EIV system, and here EIVE could fill the gap.
Almost on the same day as EIVE 1.0 another supranational system of ecological indicator values in Europe has been published by Tichý et al. (2023) with a similar approach.
Thus, it will be important for vegetation scientists in Europe to understand the pros and cons of both systems to allow the wise selection of the most appropriate tool:
EIVE 1.0 is based on 31 regional EIV systems, while Tichý et al. (2023) uses 12.
Both systems provide indicator values for moisture, nitrogen/nutrients, reaction, light and temperature, while Tichý et al. (2023) additionally has a salinity indicator.
Tichý et al. (2023) aimed at using the same scales as Ellenberg et al. (1991), which means that the scales vary between indicators (1–9, 0–9, 1–12), while EIVE has a uniform interval scale of 0–10 for all indicators.
Only EIVE provides niche width in addition to niche position. Niche width is an important aspect of the niche and might be used to improve the calculation of mean indicator values per plot (e.g. by weighting with inverse niche width).
The taxonomic coverage is larger in EIVE than in Tichý et al. (2023): 14,835 vs. 8,908 accepted taxa and 11,148 vs. 8,679 species.
EIVE provides indicator values for accepted subspecies, while Tichý et al. (2023) is restricted to species and aggregates. Separate indicator values for subspecies might be important for two reasons: (a) subspecies often strongly differ in at least one niche dimension; (b) many of the taxa now considered as subspecies have been treated at species level in the regional EIV systems.
Tichý et al. (2023) added 431 species not contained in any of the source systems based on vegetation-plot data from the European Vegetation Archive (EVA; Chytrý et al. 2016) while EIVE calculated the European indicator values only for taxa occurring at least in one source system.
While both systems present maps that suggest a good coverage across Europe, Tichý et al. (2023)’s source systems largely were from Central Europe, NW Europe and Italy, but, unlike EIVE, these authors did not use source systems from the more “distal” parts of Europe, such as Sweden, Faroe Islands, Russia, Georgia, Romania, Poland and Spain, and they used only a small subset of indicators of the EIV systems of Ukraine, Greece and the Alps.
In a validation with GBIF-derived data on temperature niches, Dengler et al. (2023) showed that EIVE has a slightly stronger correlation than Tichý et al. (2023)’s indicators (r = 0.886 vs. 0.852).
How did EIVE manage to integrate all EIV systems in Europe that contained at least one of the selected indicators for vascular plants, while Tichý et al. (2023) used only a small subset?
This difference is mainly due to a more complex workflow in EIVE (which also was one of the reasons why the preparation took so long). First, Tichý et al. (2023) restricted their search to EIV systems and indicators that had the same number of categories as the “original” Ellenberg system.
Second, from these they discarded those that showed a too low correlation with Ellenberg. By contrast, EIVE’s workflow allowed the use of any system with an ordinal (or even metric) scale, irrespective of the number of categories or the initial match with Ellenberg et al. (1991).
EIVE also did not treat one system (Ellenberg) as the master to assess all others but considered each of them equally valid. While indeed the individual EIV systems are often quite inconsistent, i.e. even if they refer to Ellenberg, the same value of an indicator in one system might mean something different in another system, our iterative linear optimisation enabled us to adjust all 31 systems for the five indicators to a common basis.
This in turn allowed deriving EIVE as the consensus system of all the source systems. The fact that in our validation of the temperature indicator, EIVE performed better than Tichý et al. (2023) and much better than most of the regional EIV systems might be attributable to the so-called “wisdom of the crowd”, going back to the statistician Francis Galton who found that averaging numerous independent assessments (even by laymen) of a continuous quantity can leads to very good estimates of the true value.
Apart from the indicator values themselves, EIVE has a second main feature that might not be so obvious at first glance, but which actually took the EIVE team, including several taxonomists, more time than the workflow to generate the indicator values themselves: the taxonomic backbone. EIVE for vascular plants is fully based on the taxonomic concept (including the synonymic relationships) of the Euro+Med Plantbase.
However, since Euro+Med lacks an important part of taxa that are frequently recorded in vegetation plots, to make our backbone fully usable to vegetation science, we expanded it beyond Euro+Med to something called “Euro+Med augmented”. We particularly added hybrids, neophytes and aggregates, three groups of plants hitherto only very marginally covered in Euro+Med. All additions were done by experts consistently with the taxonomic concept of Euro+Med and are fully documented. Likewise, many additional synonym relationships had to be added that were missing in Euro+Med.
Finally, we implemented the so-called “concept synonymy” (see Jansen and Dengler 2010), which allows the assignment of the same name from different sources to different accepted names (“taxonomic concepts”). This applies mainly to nested taxa that are treated at different levels in different sources, e.g. once as species with several subspecies, once as aggregate with several species. However, there are also some cases of misapplied names (i.e. names that were not used in agreement with their nomenclatural type in certain EIV systems). Such cases generally cannot be solved by the various tools for automatic taxonomic cleaning, but require experts who make a case-by-case decision.
The whole taxonomic workflow of EIVE is fully transparent with an R code that “digests”:
(a) the names as they are in the source systems,
(b) the official Euro+Med database and
(c) tables that document our additions and modifications (with reasons and references).
This comprehensive documentation will allow continuous and efficient improvement in the future, be it because of taxonomic novelties adopted in Euro+Med or because EIVE’s experts decide to change certain interpretations. That way, “Euro+Med augmented” and the accompanying R-based workflow can also be a valuable tool for other projects that wish to harmonise plant taxonomic information from various sources at a continental scale, e.g. in vegetation-plot databases such as GrassPlot (Dengler et al. 2018) and EVA (Chytrý et al. 2016).
The publication of EIVE 1.0 is not the endpoint, but rather a starting point for future developments in a community-based approach.
Together with interested colleagues from outside, the EIVE core team plans to prepare better and more comprehensive releases of EIVE in the future, including updates to its taxonomic backbone.
Future releases of EIVE will be published in fixed versions, typically together with a paper that describes the changes in the content.
As steps for the next two years, we anticipate that we will first add further taxa (bryophytes, lichens, macroalgae) and some additional indicators, both of which are relatively easy with our established R-based workflow. Then we plan EIVE 2.0 that will use the approx. 2 million vegetation plots in EVA (Chytrý et al. 2016) to re-calibrate EIVE for all taxa (see http://euroveg.org/requests/EVA-data-request-form-2022-02-10-Dengleretal.pdf).
This Behind the paper post refers to the article Ecological Indicator Values for Europe (EIVE) 1.0 by Jürgen Dengler, Florian Jansen, Olha Chusova, Elisabeth Hüllbusch, Michael P. Nobis, Koenraad Van Meerbeek, Irena Axmanová, Hans Henrik Bruun, Milan Chytrý, Riccardo Guarino, Gerhard Karrer, Karlien Moeys, Thomas Raus, Manuel J. Steinbauer, Lubomir Tichý, Torbjörn Tyler, Ketevan Batsatsashvili, Claudia Bita-Nicolae, Yakiv Didukh, Martin Diekmann, Thorsten Englisch, Eduardo Fernandez Pascual, Dieter Frank, Ulrich Graf, Michal Hájek, Sven D. Jelaska, Borja Jiménez-Alfaro, Philippe Julve, George Nakhutsrishvili, Wim A. Ozinga, Eszter-Karolina Ruprecht, Urban Šilc, Jean-Paul Theurillat, and François Gillet published in Vegetation Classification and Survey (https://doi.org/10.3897/VCS.98324).
Follow the Vegetation Classification and Survey journal on Facebook and Twitter.
Brief personal summaries:
Jürgen Dengler is a Professor of Vegetation Ecology at the Zurich University of Applied Science (ZHAW) in Wädenswil, Switzerland. Among others, he cofounded the European Vegetation Database (EVA), the global vegetation-plot database “sPlot” and the “GrassPlot” database of the Eurasian Dry Grassland Group. His major research interests are grassland ecology, grassland conservation, biodiversity patterns, macroecology, vegetation change, broad-scale vegetation classification, methodological developments in vegetation ecology and ecoinformatics.
Florian Jansen is a Professor of Landscape Ecology at the University of Rostock, Germany. His research interests are vegetation ecology and dynamics, mire ecology including greenhouse gas emissions, and numerical ecology with R. He (co-)founded the German Vegetation Database vegetweb.de, the European Vegetation Database (EVA), and the global vegetation-plot database “sPlot”. He wrote the R package eHOF for modelling species response curves along one-dimensional ecological gradients.
François Gillet is an Emeritus Professor of Community Ecology at the University of Franche-Comté in Besançon, France. His major research interests are vegetation diversity, ecology and dynamics, grassland and forest ecology, integrated synusial phytosociology, numerical ecology with R, dynamic modelling of social-ecological systems.
Chytrý, M., Hennekens, S.M., Jiménez-Alfaro, B., Knollová, I., Dengler, J., Jansen, F., Landucci, F., Schaminée, J.H.J., Aćić, S., (…) & Yamalov, S. 2016. European Vegetation Archive (EVA): an integrated database of European vegetation plots. Applied Vegetation Science 19: 173–180.
Dengler J, Wagner V, Dembicz I, García-Mijangos I, Naqinezhad A, Boch S, Chiarucci A, Conradi T, Filibeck G, … Biurrun I (2018) GrassPlot – a database of multi-scale plant diversity in Palaearctic grasslands. Phytocoenologia 48: 331–347.
Dengler, J., Jansen, F., Chusova, O., Hüllbusch, E., Nobis, M.P., Van Meerbeek, K., Axmanová, I., Bruun, H.H., Chytrý, M., (…) & Gillet, F. 2023. Ecological Indicator Values for Europe (EIVE) 1.0. Vegetation Classification and Survey 4: 7–29.
Ellenberg H, Weber HE, Düll R, Wirth V, Werner W, Paulißen D (1991) Zeigerwerte von Pflanzen in Mitteleuropa. Scripta Geobotanica 18: 1–248.
Jansen F, Dengler J (2010) Plant names in vegetation databases – a neglected source of bias. Journal of Vegetation Science 21: 1179–1186.
Midolo, G., Herben, T., Axmanová, I., Marcenò, C., Pätsch, R., Bruelheide, H., Karger, D.N., Acic, S., Bergamini, A., Bergmeier, E., Biurrun, I., Bonari, G., Carni, A., Chiarucci. A., De Sanctis, M., Demina, O., (…), Dengler, J., (…) & Chytrý, M. 2023. Disturbance indicator values for European plants. Global Ecology and Biogeography 32: 24–34.
Scherrer D, Guisan A (2019) Ecological indicator values reveal missing predictors of species distributions. Scientific Reports 9: Article 3061.
Tichý, L, Axmanová, I., Dengler, J., Guarino, R., Jansen, F., Midolo, G., Nobis, M.P., Van Meerbeek, K., Aćić, S., (…) & Chytrý, M. 2023. Ellenberg-type indicator values for European vascular plant species. Journal of Vegetation Science 34: e13168.
In an age where we more than ever need to appreciate and preserve the magnificent biodiversity inhabiting the Earth, we decided to go for a lighter and fun take on the work of taxonomists that often goes unnoticed by the public.
From the ocean depths surrounding Indonesia to the foliage of the native forests of Príncipe Island and into the soils of Borneo, we started with 16 species described as new to science in journals published by Pensoft over the years.
Out of these most amazing creatures, over the past several weeks we sought to find who’s got the greatest fandom by holding a poll on Twitter (you can follow it further down here or via #NewSpeciesShowdown).
While we need to admit that we ourselves expected to crown an animal as the crowd-favourite, we take the opportunity to congratulate the botanists amongst our fans for the well-deserved win of Nepenthes pudica (see the species description)!
Find more about the curious one-of-a-kind pitcher plant in this blog post, where we announced its discovery following the new species description in PhytoKeys in June 2022:
What’s perhaps even more curious, is that there is only one species EVER described in a Pensoft-published journal that has so far triggered more tweets than the pitcher plant, and that species is the animal that has ended up in second place in the New Species Showdown: a tiny amphibian living in Peru, commonly known as the the Amazon Tapir Frog (Synapturanus danta).Which brings us once again to the influence of botanists in taxonomic research.
Read more about its discovery in the blog post from February 2022:
Another thing that struck us during the tournament was that there was only one species described in our flagship journal in systematic journal ZooKeys: the supergiant isopod Bathynomus raksasa, that managed to fight its way to the semi-finals, where it lost against S. danta.
This makes us especially proud with our diverse and competitive journal portfolio full of titles dedicated to biodiversity and taxonomic research!
Twice a week, @Pensoft would announce a match between two competing species on Twitter using the hashtag #NewSpeciesShowdown, where everyone could vote in the poll for their favourie.
This competition is for entertainment purposes only. As it was tremendously tough to narrow the list down to only sixteen species, we admit that we left out a lot of spectacular creatures.
To ensure fairness and transparency, we made the selection based on the yearly Altmetric data, which covers articles in our journals published from 2010 onwards and ranks the publications according to their online mentions from across the Web, including news media, blogs and social networks.
We did our best to diversify the list as much as possible in terms of taxonomic groups. However, due to the visual-centric nature of social media, we gave preference to immediately attractive species.
(in chronological order)
Round 2 – Quarter-finals
Round 3 – Semi-finals
But why did we hold the tournament right now?
If you have gone to the Pensoft website at any point in 2022, visited our booth at a conference, or received a newsletter from any of our journals, by this time, you must be well aware that in 2022 – more precisely, on 25 December – we turned 30. And we weren’t afraid to show it!
Indeed, 30 is not that big of a number, as many of us adult humans can confirm. Yet, we take pride in reminiscing about what we’ve done over the last three decades.
Long story short, we wanted to do something special and fun to wrap up our anniversary year. While we have been active in various areas, including development of publishing technology concerning open and FAIR access and linkage for research outcomes and underlying data; and multiple EU-supported scientific projects, we have always been associated with our biodiversity journal portfolio.
Besides, who doesn’t like to learn about the latest curious creature that has evaded scientific discovery throughout human history up until our days? 😉
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
Bangladesh, Myanmar, Nepal, New Guinea and India
Southern and Central American
Guatemala, Honduras, El Salvador, Nicaragua, Bolivia, Argentina and Brazil
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.
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.
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.
“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. “
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.
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.
While every Flora publication is an incredibly valuable scientific resource, Vol. 45 is the first in the series to be made available in digital format, following its publication in the open-access journal PhytoKeys
The 45th volume of the Flora of Cameroon pilots a novel “Flora” section in the journal to promote accessibility and novelty in plant taxonomy
Dedicated to Annonaceae, the 45th volume of the Flora of Cameroon is the result of over 15 years of work on the systematics of this major pantropical group, commonly known as the Custard apple family or the Soursop family, and its diversity in one of the most biodiverse African countries, whose flora has remained understudied to this date.
In their publication, the authors: Thomas L. P. Couvreur, Léo-Paul M. J. Dagallier, Francoise Crozier, Jean-Paul Ghogue, Paul H. Hoekstra, Narcisse G. Kamdem, David M. Johnson, Nancy A. Murray and Bonaventure Sonké, describe 166 native taxa representing 163 species in 28 native genera, including 22 species known solely from Cameroon. The team also provides keys to all native genera, species, and infraspecific taxa, while a detailed morphological description and a distributional map are provided for each species.
Amongst the findings featured in the paper is the discovery of a previously unknown species of a rare tree that grows up to 6 metres and is so far only known from two localities in Cameroon. As a result of their extensive study, the authors also report that the country is the one harbouring the highest number of African species for the only pantropical genus of Annonaceae: Xylopia.
While every Flora publication presents an incredibly valuable scientific resource due to its scale and exhaustiveness, what makes Volume 45 of the Flora of Cameroon particularly special and important is that it is the first in the series to be made available in digital format, following its publication in the peer-reviewed, open-access journal PhytoKeys.
As such, it is not only available to anyone, anywhere in the world, but is also easily discoverable and minable online, as it benefits from the technologically advanced publishing services provided by the journal that have been specially designed to open up biodiversity data. While the full-text publication is machine-readable, hence discoverable by search algorithms, various data items, such as nomenclature, descriptions, images and occurrences, are exported in relevant specialised databases (e.g. IPNI, Plazi, Zenodo, GBIF). In their turn, the readers who access the HTML version of the publication may enjoy the benefits of this semantically enriched format, as they navigate easily within the text, and access further information about the mentioned and hyperlinked taxa.
In fact, the Annonaceae contribution is the first to use the newly launched publication type in PhytoKeys: Flora.
Yet, to keep up with the much treasured tradition, the new publication is also available in print format, accompanied by its classic cover design.
When we spoke with the team behind the Flora, we learnt that they are all confident that having the new volume in both print and open-access digital formats, is expected to rekindle the interest in the series, especially amongst younger botanists in Cameroon.
“The hybrid publication is a response to the reluctance to publish new volumes of these series. The hybrid version pioneered in Volume 45, is an opportunity for any scientist to freely access this fundamental work, and eventually use it in future studies. Also, the online and open access format is intended to stimulate botanists to author family treatments without the fear of not having their work published online in an academic journal with an Impact Factor,”
“The chosen format marks a qualitative leap in the presentation of the Flora of Cameroon and will be of interest to young botanists, who until now might have found the old presentation of the Flora unrewarding,” adds Prof. Bonaventure Sonké, last author and Head of the Biology Department of the Université de Yaoundé 1, Cameroon.
As an extensive contribution to a previously understudied area of research, the value of the new publication goes beyond its appreciation amongst plant taxonomists.
“The Flore du Cameroun series is considered as a showcase of the National Herbarium of Cameroon, which promotes knowledge of the flora of Cameroon at all levels. Being able to identify plants and trees is the first and foremost step to addressing the issue of ill-management of forest regions in Cameroon and the Congo Basin as a whole. If planning continues to rely on badly made identification, the forecasts about our resources are not good at all,” says Prof. Jean Betti Largarde, Head of the National Herbarium of Cameroon, and Editor-in-Chief of the Flora of Cameroon.
“Plant taxonomy is the basic discipline for the knowledge, conservation and sustainable management of biodiversity, including animals, plants and habitats. Young Cameroonian botanists, privileged to having such floristic richness in their country, are invited to take an interest in it. This is the field that opens the mind and makes it possible to address all other aspects of botanical research and development in relation to natural resources,”
adds Jean Michel Onana.
Couvreur TLP, Dagallier L-PMJ, Crozier F, Ghogue J-P, Hoekstra PH, Kamdem NG, Johnson DM, Murray NA, Sonké B (2022) Flora of Cameroon – Annonaceae Vol 45. PhytoKeys 207: 1-532. https://doi.org/10.3897/phytokeys.207.61432
Microbes growing on flowers have adverse effects on their fruit yields. This is why plants are quick to shed their flowers, reveals a new study involving both field experiments and plant microbiome analyses.
Microbes growing on flowers have adverse effects on their yields. This is why plants are quick to shed their flowers, reveals a new study involving both field experiments and plant microbiome analysis.
Scientifically speaking, flowers are a reproductive structure of a plant. Unlike mammals, though, perennial plants develop those de novo every season and only retain them for as long as needed.
While a few earlier studies have already looked into the variation in flower lifespan among species, they were mainly concerned with the tradeoff between plants spending energy on producing and maintaining their flowers, and the benefit they would achieve from retaining their reproductive organs.
Prior to the present study, however, the team found another perspective to look at the phenomenon: why did plants invest their energy – even if the ‘cost’ was minimal – to produce fragile flowers that would wither in a matter of days, rather than investing a bit more of it to produce a lot more durable ones, thereby increasing their reproductive success?
Flowers provide various habitats for microbes. They attract pollinators by secreting nectar, which is rich in sugars, and often contains other nutrients, such as amino acids and lipids. The stigma is a germination bed for pollen grains connected to a growth chamber for pollen tubes. It maintains humidity and nutrients necessary for pollen tube growth. Not surprisingly, abundance of the microbes increases over time on individual flowers after it opens.
Before jumping to their conclusions, the scientists set out to conduct field experiments to see what microbial communities would appear on flowers if their longevity was prolonged.
To do this, they took microbes from old flowers of wild ginger (Alpinia japonica) – a species found in Japan and blooming in the early summer when the hot and humid weather in the country is ideal for microbial growth. Then, they transferred the microbes to other wild ginger plants, whose flowers had just opened.
In line with their initial hypothesis, the research team noted that the plant produced significantly fewer fruits, yet there were no visible symptoms on the flowers or fruits to suggest a disease. However, an analysis of the plants’ microbiomes revealed the presence of several groups of bacteria that were increasing with time. As these bacteria can also be found on the flower buds of flowers that have not been treated, the bacteria is categorised as “resident” for the plant.
“So far, flower characteristics have mostly been studied in the context of their interactions with pollinators. Recent studies have raised the question whether we have overlooked the roles of microbes in the studies of floral characteristics.
For example, flower volatiles – which are often regarded as a primary pollinator attractant – can also function to suppress antagonistic microbes. The impacts of microbes on plant reproductive ecology may be more deeply embedded in the evolution of angiosperms than we have considered,”
Jiménez Elvira N, Ushio M, Sakai S (2022) Are microbes growing on flowers evil? Effects of old flower microbes on fruit set in a wild ginger with one-day flowers, Alpinia japonica (Zingiberaceae). Metabarcoding and Metagenomics 6: e84331. https://doi.org/10.3897/mbmg.6.84331
Follow the Metabarcoding and Metagenomics (MBMG) journal on Twitter and Facebook (@MBMGJournal).
Ask any scientist — for every “Eureka!” moment, there’s a lot of less-than-glamorous work behind the scenes. Making discoveries about everything from a new species of dinosaur to insights about climate change entails some slogging through seemingly endless data and measurements that can be mind-numbing in large doses.
Community science shares the burden with volunteers who help out, for even just a few minutes, on collecting data and putting it into a format that scientists can use. But the question remains how useful these data actually are for scientists.
A new study, authored by a combination of high school students, undergrads and grad students, and professional scientists showed that when museum-goers did a community science activity in an exhibit, the data they produced were largely accurate, supporting the argument that community science is a viable way to tackle big research projects.
“We were able to combine a small piece of the Field Museum’s vast collections, their scientific knowledge and exhibit creation expertise, the observational skills of biology interns at Northeastern Illinois University (USA), led by our collaborator Tom Campbell, and our Roosevelt University student’s data science expertise. The creation of this set of high-quality data was a true community effort!”
The study focuses on an activity in an exhibition at the Field Museum, in which visitors could partake in a community science project. In the community science activity, museumgoers used a large digital touchscreen to measure the microscopic leaves photographs of plants called liverworts.
These tiny plants, the size of an eyelash, are sensitive to climate change, and they can act like a canary in a coal mine to let scientists know about how climate change is affecting a region. It’s helpful for scientists to know what kinds of liverworts are present in an area, but since the plants are so tiny, it’s hard to tell them apart. The sizes of their leaves (or rather, lobes — these are some of the most ancient land plants on Earth, and they evolved before true leaves had formed) can hint at their species. But it would take ages for any one scientist to measure all the leaves of the specimens in the Field’s collection. Enter the community scientists.
“Drawing a fine line to measure the lobe of a liverwort for a few hours can be mentally strenuous, so it’s great to have community scientists take a few minutes out of their day using fresh eyes to help measure a plant leaf. A few community scientists who’ve helped with classifying acknowledged how exciting it is knowing they are playing a helping hand in scientific discovery,”
says Heaven Wade, a research assistant at the Field Museum who began working on the MicroPlants project as an undergraduate intern.
Community scientists using the digital platform measured thousands of microscopic liverwort leaves over the course of two years.
“At the beginning, we needed to find a way to sort the high quality measurements out from the rest. We didn’t know if there would be kids drawing pictures on the touchscreen instead of measuring leaves or if they’d be able to follow the tutorial as well as the adults did. We also needed to be able to automate a method to determine the accuracy of these higher quality measurements,”
To answer these questions, Pivarski worked with her students at Roosevelt University to analyze the data. They compared measurements taken by the community scientists with measurements done by experts on a couple “test” lobes; based on that proof of concept, they went on to analyze the thousands of other leaf measurements. The results were surprising.
“We were amazed at how wonderfully children did at this task; it was counter to our initial expectations. The majority of measurements were high quality. This allowed my students to create an automated process that produced an accurate set of MicroPlant measurements from the larger dataset,”
The researchers say that the study supports the argument that community science is valuable not just as a teaching tool to get people interested in science, but as a valid means of data collection.
Pivarski M, von Konrat M, Campbell T, Qazi-Lampert AT, Trouille L, Wade H, Davis A, Aburahmeh S, Aguilar J, Alb C, Alferes K, Barker E, Bitikofer K, Boulware KJ, Bruton C, Cao S, Corona Jr. A, Christian C, Demiri K, Evans D, Evans NM, Flavin C, Gillis J, Gogol V, Heublein E, Huang E, Hutchinson J, Jackson C, Jackson OR, Johnson L, Kirihara M, Kivarkis H, Kowalczyk A, Labontu A, Levi B, Lyu I, Martin-Eberhardt S, Mata G, Martinec JL, McDonald B, Mira M, Nguyen M, Nguyen P, Nolimal S, Reese V, Ritchie W, Rodriguez J, Rodriguez Y, Shuler J, Silvestre J, Simpson G, Somarriba G, Ssozi R, Suwa T, Syring C, Thirthamattur N, Thompson K, Vaughn C, Viramontes MR, Wong CS, Wszolek L (2022) People-Powered Research and Experiential Learning: Unravelling Hidden Biodiversity. Research Ideas and Outcomes 8: e83853. https://doi.org/10.3897/rio.8.e83853
From 1973 to 2020, Australian zoologist Dr Robert Mesibov kept careful records of the “where” and “when” of his plant and invertebrate collecting trips. Now, he has made those valuable biodiversity data freely and easily accessible via the Zenodo open-data repository, so that future researchers can rely on this “authority file” when using museum specimens collected from those events in their own studies. The new dataset is described in the open-access, peer-reviewed Biodiversity Data Journal.
While checking museum records, Dr Robert Mesibov found there were occasional errors in the dates and places for specimens he had collected many years before. He was not surprised.
One solution to this problem was what librarians and others have long called an “authority file”.
“It’s an authoritative reference, in this case with the correct details of where I collected and when”, he explained.
“I kept records of almost all my collecting trips from 1973 until I retired from field work in 2020. The earliest records were on paper, but I began storing the key details in digital form in the 1990s.”
The 48-year record has now been made publicly available via the Zenodo open-data repository after conversion to the Darwin Core data format, which is widely used for sharing biodiversity information. With this “authority file”, described in detail in the open-access, peer-reviewed Biodiversity Data Journal, future researchers will be able to rely on sound, interoperable and easy to access data, when using those museum specimens in their own studies, instead of repeating and further spreading unintentional errors.
“There are 3829 collecting events in the authority file”, said Mesibov, “from six Australian states and territories. For each collecting event there are geospatial and date details, plus notes on the collection.”
Mesibov hopes the authority file will be used by museums to correct errors in their catalogues.
“It should also save museums a fair bit of work in future”, he explained. “No need to transcribe details on specimen labels into digital form in a database, because the details are already in digital form in the authority file.”
Mesibov points out that in the 19th and 20th centuries, lists of collecting events were often included in the reports of major scientific expeditions.
“Those lists were authority files, but in the pre-digital days it was probably just as easy to copy collection data from specimen labels.”
“Authority files for collecting events are the next logical step,” said Mesibov. “They can be used as lookup tables for all the important details of individual collections: where, when, by whom and how.”