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BIOfid is a specialized information service currently being developed to mobilize biodiversity data dormant in printed historical and modern literature and to offer a platform for open access journals on the science of biodiversity. Our team of librarians, computer scientists and biologists produce high-quality text digitizations, develop new text-mining tools and generate detailed ontologies enabling semantic text analysis and semantic search by means of user-specific queries. In a pilot project we focus on German publications on the distribution and ecology of vascular plants, birds, moths and butterflies extending back to the Linnaeus period about 250 years ago. The three organism groups have been selected according to current demands of the relevant research community in Germany. The text corpus defined for this purpose comprises over 400 volumes with more than 100,000 pages to be digitized and will be complemented by journals from other digitization projects, copyright-free and project-related literature. With TextImager (Natural Language Processing & Text Visualization) and TextAnnotator (Discourse Semantic Annotation) we have already extended and launched tools that focus on the text-analytical section of our project. Furthermore, taxonomic and anatomical ontologies elaborated by us for the taxa prioritized by the project’s target group - German institutions and scientists active in biodiversity research - are constantly improved and expanded to maximize scientific data output. Our poster describes the general workflow of our project ranging from literature acquisition via software development, to data availability on the BIOfid web portal (http://biofid.de/), and the implementation into existing platforms which serve to promote global accessibility of biodiversity data.
Thirty-seven alien plant species, pre-identified by horizon scanning exercises were prioritised for pest risk analysis (PRA) using a modified version of the EPPO Prioritisation Process designed to be compliant with the EU Regulation 1143/2014. In Stage 1, species were categorised into one of four lists – a Residual List, EU List of Minor Concern, EU Observation List and the EU List of Invasive Alien Plants. Only those species included in the latter proceeded to the risk management stage where their priority for PRA was assessed. Due to medium or high spread potential coupled with high impacts twenty-two species were included in the EU List of Invasive Alien Plants and proceeded to Stage 2. Four species (Ambrosia trifida, Egeria densa, Fallopia baldschuanica and Oxalis pes-caprae) were assigned to the EU Observation List due to moderate or low impacts. Albizia lebbeck, Clematis terniflora, Euonymus japonicus, Lonicera morrowii, Prunus campanulata and Rubus rosifolius were assigned to the residual list due to a current lack of information on impacts. Similarly, Cornus sericea and Hydrilla verticillata were assigned to the Residual List due to unclear taxonomy and uncertainty in native status, respectively. Chromolaena odorata, Cryptostegia grandiflora and Sphagneticola trilobata were assigned to the Residual List as it is unlikely they will establish in the Union under current climatic conditions. In the risk management stage, Euonymus fortunei, Ligustrum sinense and Lonicera maackii were considered a low priority for PRA as they do not exhibit invasive tendencies despite being widely cultivated in the EU over several decades. Nineteen species were identified as having a high priority for a PRA (Acacia dealbata, Ambrosia confertiflora, Andropogon virginicus, Cardiospermum grandiflorum, Celastrus orbiculatus, Cinnamomum camphora, Cortaderia jubata, Ehrharta calycina, Gymnocoronis spilanthoides, Hakea sericea, Humulus scandens, Hygrophila polysperma, Lespedeza cuneata, Lygodium japonicum, Pennisetum setaceum, Prosopis juliflora, Sapium sebiferum, Pistia stratiotes and Salvinia molesta).
Nature affects human well-being in multiple ways. However, the association between species diversity and human well-being at larger spatial scales remains largely unexplored. Here, we examine the relationship between species diversity and human well-being at the continental scale, while controlling for other known drivers of well-being. We related socio-economic data from more than 26,000 European citizens across 26 countries with macroecological data on species diversity and nature characteristics for Europe. Human well-being was measured as self-reported life-satisfaction and species diversity as the species richness of several taxonomic groups (e.g. birds, mammals and trees). Our results show that bird species richness is positively associated with life-satisfaction across Europe. We found a relatively strong relationship, indicating that the effect of bird species richness on life-satisfaction may be of similar magnitude to that of income. We discuss two, non-exclusive pathways for this relationship: the direct multisensory experience of birds, and beneficial landscape properties which promote both bird diversity and people's well-being. Based on these results, this study argues that management actions for the protection of birds and the landscapes that support them would benefit humans. We suggest that political and societal decision-making should consider the critical role of species diversity for human well-being.
Background: The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text.
Results: We have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits of plant species found in Floras. We used the Plant Ontology (PO) and the Phenotype And Trait Ontology (PATO) to extract entity-quality relationships from digitized taxon descriptions in Floras, and used a formal ontological approach based on phenotype description patterns and automated reasoning to generate the FLOPO. The resulting ontology consists of 25,407 classes and is based on the PO and PATO. The classified ontology closely follows the structure of Plant Ontology in that the primary axis of classification is the observed plant anatomical structure, and more specific traits are then classified based on parthood and subclass relations between anatomical structures as well as subclass relations between phenotypic qualities.
Conclusions: The FLOPO is primarily intended as a framework based on which plant traits can be integrated computationally across all species and higher taxa of flowering plants. Importantly, it is not intended to replace established vocabularies or ontologies, but rather serve as an overarching framework based on which different application- and domain-specific ontologies, thesauri and vocabularies of phenotypes observed in flowering plants can be integrated.
To understand the rapid rate of change in global biodiversity, it is necessary to analyse the present condition of ecosystems and to elucidate relationships of species to their environment. The BIOKLIM Project (Biodiversity and Climate Change Project) is intended to close this gap in our knowledge of montane and high montane forests of Central European low mountain ranges, one of the most threatened mixed montane systems worldwide. The Bavarian Forest National Park is characterised by its altitude range of ca. 800 m and a strongly developed gradient of forest structure. Relicts of old growth forests (areas of former local nature reserves) and dead stands, mostly killed by bark beetles, are accompanied by widely varying levels of woody debris and light. The gradients comprise a wide range of abiotic and forest structure factors, making the study area well suited for a multidisciplinary investigation of biodiversity. Unconstrained ordination (CA) of six taxa (vascular plants, wood inhabiting fungi, birds, carabids, spiders and molluscs) indicate the altitudinal gradient to be the main driver for distribution patterns of species assemblages. Objectives, structure, study design and data sampling of the BIOKLIM Project are described in detail. We set up 293 sampling plots along four main straight transects following the altitudinal gradient. All abiotic and stand structure data regarded as relevant are available for each plot. Vascular plants, wood inhabiting fungi and birds were sampled or mapped on all 293 plots. For the other 22 investigated taxa we used subsamples pre-stratified according to the sampling methods. The necessity of dealing with spatial autocorrelation, arising from sampling along linear transects, is described. Finally, study approach of our biodiversity project is compared with others involving altitudinal gradients. Worldwide, only a few multidisciplinary biodiversity studies have been previously conducted on long altitudinal gradients. However, in most cases sampling techniques were similar to ours, which allows comparison of results between continents. Keywords: Climate Change, Biodiversity, species-environment relationships
The large number of species still to be discovered in fungi, together with an exponentially growing number of environmental sequences that cannot be linked to known taxa, has fuelled the idea that it might be necessary to formally name fungi on the basis of sequence data only. Here we object to this idea due to several shortcomings of the approach, ranging from concerns regarding reproducibility and the violation of general scientific principles to ethical issues. We come to the conclusion that sequence-based nomenclature is potentially harmful for mycology as a discipline. Additionally, a classification based on sequences as types is not within reach anytime soon, because there is a lack of consensus regarding common standards due to the fast pace at which sequencing technologies develop.
Nature benefits human health. To date, however, little is known whether biodiversity relates to human health. While some local and city level studies show that species diversity, as a measure of biodiversity, can have positive effects, there is a lack of studies about the relationship between different species diversity measures and human health, especially at larger spatial scales. Here, we conduct cross-sectional analyses of the association between species diversity and human health across Germany, while controlling for socio-economic factors and other nature characteristics. As indicators for human health, we use the mental (MCS) and physical health (PCS) component scales of the German Socio-Economic Panel (SOEP, Short Form Health Questionnaire – SF12). For species diversity, we use species richness and abundance estimates of two species groups: plants and birds. We phrase the following hypotheses: plant and bird species are positively associated with mental and physical health (H1 & H3); bird abundance is positively related to mental health (H2). Our results demonstrate a significant positive relationship between plant and bird species richness and mental health across all model variations controlling for a multitude of other factors. These results highlight the importance for species diversity for people’s mental health and well-being. Therefore, policy makers, landscape planners and greenspace managers on the local and national level should consider supporting biodiverse environments to promote mental health and wellbeing. For this purpose, we propose to use species diversity measures as indicators for salutogenic (health promoting) characteristics of nature, landscape and urban green space.
Revision of the genus Cerapanorpa (Mecoptera: Panorpidae) with descriptions of four new species
(2019)
The genus Cerapanorpa Gao, Ma & Hua, 2016 is taxonomically revised. Cerapanorpa is confirmed to be endemic to the mountain regions in central China. Nineteen species are recognized in the genus, including four new species: Cerapanorpa baimaensis sp. nov., Cerapanorpa xuebaodinga sp. nov., and Cerapanorpa yanggashana sp. nov. from the Minshan Mountains, and Cerapanorpa taizishana sp. nov. from the northeastern margin of the Qinghai-Tibetan Plateau. Six species are transferred from Cerapanorpa back to Panorpa Linnaeus, 1758. An updated key to species is presented.
Umborotula bogorensis (Weber, 1890) is a freshwater sponge species that is recorded occasionally, mainly on islands and peninsulas of Australasia. Less than 10 records with morphological descriptions and illustrations have been published so far, and the most recent record is dated 1978. A list of the few voucher specimens from museum collections is provided here together with the rich unpublished Sasaki collection from Japan, Korea, and Taiwan, recently deposited in a Japanese museum. The present new record from Northeast Thailand enlarges the geographic range of U. bogorensis to the Indochina mainland. A comparison of historical data vs present Thai records is performed by morpho-analysis(SEM) as well as biogeographic, ecological and climatic data. Results show low variability in shape and size of the diagnostic morphotraits in populations scattered over the wide geographic range. Here we also formally accept the new taxonomic status (rank elevation) of the previous suborder Spongillina as a new order Spongillida. The presence of this potentially threatened species in the Sakaerat Biosphere Reserve, together with its possible long-term persistence in the Bogor Botanical Garden, may support its conservation. Only a census of the known, extremely scattered populations will define the status of this species.
Insect taxonomy is fundamental to global biodiversity research, but few studies have been conducted to track progress in this field using objective criteria. This study reports publishing trends in the taxonomy of four diverse, globally-distributed insect families from 1946 to 2012 to elucidate recent progress and the current status of insect taxonomy. Publications included in the Zoological Record online literature database were analyzed for Cicadellidae (leafhoppers), Miridae (plant bugs), Pyralidae (moths) and Staphylinidae (rove beetles). Data on numbers of new species, article length, species description length, authorship and collaborations, and taxonomic journals were extracted and compiled for each year. The results showed that (1) the number of taxonomic papers increased before 1980, followed by a steep decline with subsequent partial recovery; (2) the number of papers describing new species generally mirrored the trend in numbers of new species, suggesting no overall change in the proportion of larger, synthetic works (monographs) and more such work is encouraged; (3) the average number of new species described per publication decreased over the time period investigated, but with an increase in the average description pages per new species; (4) researchers from Europe and North America continue to produce the most taxonomic research on three of the four families, but the main center for Cicadellidae taxonomy has recently shifted to Asia; (5) collaboration among authors within and across continents has increased as indicated by increases in coauthored papers; and (6) journal prevalence differed for the four families and the top 10 most utilized journals for each family were given out for reference. Based on the analysis of the publication trend of the four families, we found that the overall trend toward increasing rates of species discovery is encouraging. But more human resources training and financial support on taxonomic work are required in order to complete a global faunistic inventory in a reasonable timeframe. Future study that conducts more in-depth and comprehensive analysis based on more families is required to reflect the overall trend of the insect taxonomy.