Database Of Occurrences Research Articles

Reconstructing a georeferenced inventory of flooding hazards in Raoping, Guangdong province, China, from 1492 to 1985

ABSTRACT In ancient times, there is a scarcity of instrumental water flow data, which challenges the hydrological science community to understand the evolution of flood risk under the changing climate over the centennial scale. Based on the historical records of flood events, the first spatio-temporal database of flood risk occurrence was established in Raoping county, Guangdong, China from 1492 to 1985 (a 494-year period), with intensive human interpretation and local investigation. Specifically, the spatially explicit flood events of the river network were provided for each flood episode. A detailed analysis of the database shows a high frequency of flood risk in summer and early autumn. Specifically, a significant (p < 0.05) increase has been found in flood risks since 1960. However, flooding decreased significantly in recent decades due to meteorological and hydrological factors, as well as the population density and migration during the 500-year period. A spatial clustering of flood events in the northern and southern parts is also confirmed, which shows an impact of population dynamics on a centennial scale. Such methods can be a reference for establishing China's flooding database for ancient periods, promoting a better understanding of natural hazards and associated human behaviors under the context of long-term climate change.

The Effect of Railway Projects Increasing Safety on the Frequency of Occurrences

This contribution is focused on the presentation of individual research results aimed at evaluating the socio-economic impacts associated with increasing the safety and reliability of the railway transport route. The goal of the research is to propose and subsequently verify an original approach for assessing the impact of the implementation of investment projects, including measures aimed at increasing the safety and reliability of railway transport routes, on the resulting number of occurrences that happen on the railway in the Czech Republic. The proposed procedure is based on several key documents. In addition to already existing national methodologies, these are mainly the database of occurrences managed by the Railway Administration of the Czech Republic, including approximately 1000 occurrences for each year of the evaluated period (2009–2018), and information on 33 projects on the railway transport route, where the effects of their implementation on the overall frequency of occurrences are examined events in the subject location. The output of the research is a methodical approach for assessing the impact of the implementation of projects aimed at increasing the safety and reliability of the railway transport route. We perceive the impact on the occurrences from the point of view of the frequency of their occurrence and from the point of view of the socio-economic impacts that are achieved as a result of the implementation of the projects. From the point of view of the frequency of occurrence, a reduction in its value of 4.63% was found. As part of the research, the impact on the occurrence of extraordinary events is also assessed in the context of the scope of the railway transport route, both with regard to the length of the reconstructed track and also with regard to traffic performance.

Amazonian amphibians: diversity, spatial distribution patterns, conservation and sampling deficits.

The Amazon biome is home to the largest tropical forest on the planet and has the greatest global biodiversity on Earth. Despite this, several less charismatic taxonomic groups, such as amphibians, lack comprehensive studies on their species richness and spatial distribution in the Amazon Region. In this study, we investigated: i) patterns of richness and endemism of Amazonian amphibians across geopolitical and biogeographic divisions, ii) similarities between different Amazonian bioregions, iii) temporal trends in amphibian sampling, iv) conservation status of amphibians according to assessments of the IUCN and v) the importance of diverse data sources in building a robust database of amphibian occurrences. We aggregated data from four different sources: publicly accessible platforms, peer-reviewed articles, grey literature and fieldwork inventories spanning 15 years (2007-2021), ultimately compiling 160,643 records of 947 species across 7,418 sampled sites. The greatest diversity of species was found in Peru, Brazil and Ecuador, with notable amphibian diversity and endemism in regions such as the western basins and the Tapajós River Basin in the central-southern Amazon. Geographical analysis of species diversity revealed four distinct groups defined by latitudinal (the Amazon River) and longitudinal (the Juruá, Madeira and Tapajós Rivers) gradients, with low species similarity (< 40%), particularly in the basins of north-western Amazonia. Amphibian sampling in the Amazon has intensified since the 1950s with the establishment of important research centres such as INPA and the GOELD Museum in the Brazilian Amazon. Approximately 18% of Amazonian amphibian species face extinction risk, according to IUCN assessments, highlighting the need for comprehensive data sources to understand and conserve species in this megadiverse region. Our findings suggest that river systems likely influence Amazonian amphibian species composition due to biogeographic history, emphasising the need for robust taxonomic and spatial databases. This study, therefore, contributes a valuable large-scale dataset for Amazonian amphibians, guiding future research and strategies for amphibian conservation.

Geospatial Modelling of Flood Susceptibility of the Calabar City, Cross River State, Nigeria

Flooding remains a major environmental problem in many parts of the world including Nigeria, causing untold losses. This study modelled the flood susceptibility of Calabar Metropolis using frequency ratio and geographical information system (GIS). Direct field observation and key informant approaches were used to obtain 127 previous and current flood locations in the study area from which a database of historical flood occurrence was developed. Using the geostatistical analyst tool within a geographical information environment the flood locations were split into two parts in the ratio of 70:30 percent for the training and testing processes, respectively. Eight flood conditioning factors (elevation, slope, aspect, curvature topographic position index, topographic wetness index, land cover and normalized difference vegetation index) were extracted from SRTM-30m DEM and Landsat 8 data accordingly and used in the geospatial analysis of flood occurrence within the GIS. The frequency ratio model was then developed using the training dataset. The final product was the flood susceptibility map of the study area. The results revealed that 9.3 percent of the study area was considered to have very high flood susceptibility, 19.97 percent was classified as high flood susceptibility while 31.79 percent was under moderate risk area. About 39 percent of the study area was classified at least under low flood susceptibility. The order of contribution of the conditioning factors to the model were topographic position index (TPI), elevation, normalized difference vegetation index (NDVI), land cover, curvature, aspect, slope, and topographic wetness index (TWI). The validation of the model using the receiver operating characteristics (ROC) curve returned an AUC value of 74.81 percent. Hence, the result was acceptable for the prediction of flood locations in the study area. The findings would assist urban planners, environmental managers, risk reduction and management agencies, land developers, policy makers, and indeed the general public.

A Review of Training Procedures for Simulated Engine Failure after Take-Off Exercises with Twin-Engine Aircraft under 5700 kg

Engine failure after take-off (or one engine being inoperative) is an exercise conducted as part of multi-engine flight training and on-going competency checking. To prepare pilots to manage a real in-flight emergency, this exercise has traditionally been conducted immediately after take-off. This has led to increased risks of fatal accidents due to the reduced height at which these exercises are typically conducted. Yet, there is variation in the heights stipulated in training procedures published by different stakeholders worldwide. Additionally, the conduct of the exercise has resulted in fatal accidents worldwide. This paper aims to review the previous literature on aviation training and aviation occurrence data to determine what empirical data exists to support the method of conducting simulated engine failures. Peer-reviewed academic publications on aviation training, aviation occurrence databases such as aviation investigation reports, and guidance materials published by aviation authorities on simulated training exercises will be included in this paper. It was found that the previous research on these exercises has focused on the transfer of motion cues or pilot responses to abnormal situations, but did not include specific data comparing pilot performance at different heights above ground level. A review of aviation occurrences found that actual engine failures occurred at higher heights that those used in simulated engine failures. A comparison of the guidance published by aviation authorities identified variations in the minimum altitude published and differing justifications for the minimum height chosen. Future research is needed to compare pilot performance during simulated engine failures to determine the ideal height to conduct the exercise to be representative of an actual engine failure while maintaining safety margins.

Earthworm records and habitat associations in the British Isles

The National Earthworm Recording Scheme (NERS) is the most comprehensive national database of earthworm species occurrence records for the British Isles, and possibly for any individual country in the world. Utilising the NERS database, we sought to update the current knowledge of earthworm species occurrences in the UK, Ireland and Channel Islands; identify species-specific habitat and microhabitat associations; reveal any biases and complementarities between amateur naturalist and research-related earthworm record collection; and inform how future earthworm sampling can be better focussed to improve our knowledge of earthworm ecology. We found that the most commonly occurring earthworm species were present in farmland and woodland, and recovered via soil pit sampling, the most common habitat-sampling protocol combinations. However, several earthworm species showed specificity to alternative habitats (such as trees, wetlands, and compost), and association with microhabitat (non-soil) sampling. There were clear disparities between scientific researchers and amateur naturalist recorders in terms of habitat types visited and sampling protocols/microhabitats used in the collection of earthworm records. Most importantly, we found that earthworm species currently considered to be nationally ‘rare’ in the British Isles are significantly associated with the most under-represented habitat-protocol/microhabitat combinations (forest deadwood and other microhabitats, in addition to scrubland, wetland and heathland habitats), and thus may not be rare, only under-sampled. We therefore encourage earthworm researchers and recorders to give greater attention to these situations, to gain new insights into these earthworm species' ecologies and distributions. Finally, we would like to promote the establishment of earthworm recording schemes in other countries, to enable national and global collaborative monitoring of earthworm responses to environmental change.

Prototype Biodiversity Digital Twin: Phylogenetic Diversity

Phylogenetic diversity (PD) represents a fundamental measure of biodiversity, encapsulating the extent of evolutionary history within species groups. This measure, pivotal for understanding biodiversity's full dimension, has gained recognition by major environmental and scientific organisations, including the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. Unlike traditional taxonomic richness, PD offers a comprehensive, evolutionary perspective on biodiversity, essential for conservation planning and biodiversity management. This manuscript describes the development of a BioDT (Biodiversity Digital Twin) prototype, aimed at facilitating the calculation and visualisation of biodiversity metrics from global, dynamic data sources. By utilising the PhyloNext pipeline and integrating with global phylogenetic and species occurrence databases like the Open Tree of Life (OToL) and the Global Biodiversity Information Facility (GBIF), the prototype aims to significantly reduce computation time and enhance user interaction. This enables dynamic visualisation and potentially hypothesis testing, making it a valuable tool for researchers, monitoring initiatives, policy-makers and the public. The prototype's development focuses on improving the PhyloNext pipeline's scalability and creating a more intuitive user interface, expanding its utility for conservation efforts and biodiversity exploration. Our work illustrates the potential impact of the BioDT prototype in supporting diverse user groups in visualising and exploring PD, thus contributing to more informed decision-making in conservation and biodiversity management.

PROJECTED CHANGE IN DISTRIBUTION PATTERNS OF CROP WILD RELATIVES UNDER CLIMATE CHANGE: A CASE STUDY OF THE FERTILE CRESCENT

The principal aim of this paper is to evaluate alterations in the geographical distributions of priority crop wild relatives (CWRs) within the Fertile Crescent Region. The analysis encompasses a comprehensive set of 441 priority CWRs. To compile species distribution information, a meticulously constructed database of occurrence records was utilized. The process involved gathering current and projected climate data from WorldClim to facilitate the evaluation. This study employed MaxEnt version 3.4.1 for species distribution modeling (SDM) considering two distinct dispersal scenarios. One scenario proposed that the CWR taxa were incapable of adapting to their preferred weather conditions, while the other scenario suggested that CWR could track suitable climates to ensure their survival. The generated maps underwent processing in DIVA-GIS version 7.5. Notably, Aegilops bicornis, a wild relative of bread wheat, and Triticum monococcum, a wild relative of wheat, are anticipated to face substantial impacts due to climate change. Specifically, the dispersal of T. monococcum is predicted to shift toward the north, where new suitable areas are expected to emerge in Northern Iraq. Conversely, Cicer bijugum, a wild relative of chickpea, Vicia grandiflora, a wild relative of common vetch, and Beta corolliflora, a wild relative of sugar beet, are projected to experience a comparatively slight impact from climate change, as their potential distribution areas are estimated to diminish. Overall, this study foresees a decline in CWRs across the Fertile Crescent, particularly noting reduced habitats for the CWRs in Turkey.

The where, when, and how of ooid formation: What ooids tell us about ancient seawater chemistry

Ooids are a common constituent of carbonate rock throughout the last 3.2 billion years. The chemical and physical characteristics of ooids record essential details of the carbonate chemistry and hydrodynamic conditions of their depositional environment. As a result, ooids may be a powerful tool for reconstructing Earth's ancient climates and environments. However, lack of constraints on fundamental aspects of ooid formation, such as the role of abrasion, underscores the potential for additional discoveries utilizing ooids as paleoenvironmental proxies. Here, we use three-dimensional models built by serially grinding and imaging ooids to show how ooid shape changes during growth. We find that ooid abrasion plays only a small role in the formation of ooids, even in giant ooids, where the mass should cause abrasion to be most intense. A lack of abrasion during ooid formation suggests a greater sensitivity of ooid distribution and size to the chemistry of depositional environments. This insight enables us to harmonize our understanding of ooid formation with longstanding questions regarding their spatial and temporal distribution, as well as size variations. With a new database of ooid occurrences, we analyze the influence of seawater chemistry, carbonate shelf area, and evolutionary developments on ooid abundance in the Modern, Last Glacial Period, and throughout the Phanerozoic. Finally, we leverage our new understanding of ooid growth to show how ooid size, including giant ooids, can shed light on relative changes in alkalinity throughout the Phanerozoic.

Unregulated drinking water contaminants and adverse birth outcomes in Virginia

Unregulated drinking water contaminants and adverse birth outcomes in Virginia

An extensive database on the traits and occurrences of amphibian species in Turkey

Amphibians are the most endangered taxa among vertebrates, and they face many threats during their complex life cycles. The species’ life history traits and occurrence database help understand species responses against ecological factors. Consequently, the species-level-trait database has gained more prominence in recent years as a useful tool for understanding the dimensions of communities, assembly processes of communities, and conserving biodiversity at the ecosystem level against environmental changes. However, in Turkey, there are deficiencies in the knowledge of the ecological traits of amphibians compared to other vertebrate taxa, as most studies have focused on their distribution or taxonomic status. Consequently, there is a need to create such a database for future research on all known extant amphibians in Turkey. We compiled a species-level data set of species traits and occurrences for all amphibians in Turkey using 436 literature sources. We completed 36 trait categories with 5611 occurrence data for 37 amphibian species in Turkey. This study provides an open, useful, and comprehensive database for macroecological and conservation studies on amphibians in Turkey.

Increasing fish biodiversity in high elevation Albertan lakes in response to global environmental change over the past 50 years

IntroductionThe diversity of freshwater fishes is threatened by multiple environmental stressors, including climate change, alterations in land use, and introduction of non-native species. However, the quantification of temporal biodiversity in freshwater communities is limited. Here, we asked: i) how has alpha (species richness), beta (changes in freshwater species composition), and gamma diversity (total species diversity in a landscape) changed over time for lakes over a 50 year period?; and ii) What are the climatic, land use, and lake morphological drivers associated with higher diversity?MethodsWe assembled a database of fish species occurrence from 20 lakes across subalpine and alpine regions in Alberta from 1970-2019, in addition to lake morphological, climatic, and land use characteristics of the watersheds. ResultsWe observed an overall increase in alpha, beta, and gamma diversity from the 1970s to 2009s. However, all measures of diversity declined from 2010-2019. We found that more lakes and species assemblages were influenced by species gains, rather than species losses (with the exception of the last decade of sampling). DiscussionGenerally, we found that coolwater species were expanding and coldwater fishes were being lost throughout our study lakes. We highlight temporal heterogeneity in fish biodiversity responses to substantial environmental pressures in this region.

Reconstructing Cretaceous climate: Insights from a new calcareous nannofossil occurrence database.

Reconstructing Cretaceous climate: Insights from a new calcareous nannofossil occurrence database.

Climate change in open environments: Revisiting the current distribution to understand and safeguard the future of psammophilous squamates of the Diagonal of Open Formations of South America

To identify regions that contribute to the persistence of biodiversity, we (1) predict the potential distribution of the psammophilous squamate species endemic of the Diagonal of Open Formations (DOF) in the current climate, (2) identify survey priority areas, (3) estimate the impacts of climate change in two future CO2 emission scenarios, and (4) discuss strategies to safeguard these target species. We created an occurrence database and used environmental variables for the current and future periods to run the potential distribution models. We obtained models with high performance for all species and scenarios. Our study indicates potential occurrence areas for the psammophilous squamates of the DOF that still need to be sampled and are a survey priority for future inventories. In all future projections, climate change is predicted to shift the suitability and promote species range change, modifying the richness patterns for the psammophilous squamate reptiles of DOF. Finally, we demonstrate that future climatic conditions may decrease the effectiveness of current areas in protecting the diversity of these reptiles. Our results highlight the vulnerability of psammophilous squamates from South American Dry Diagonal to climate change and provide crucial information of the need of dynamic public policies for conservation of these species.

PhyloSophos: a high-throughput scientific name mapping algorithm augmented with explicit consideration of taxonomic science, and its application on natural product (NP) occurrence database processing

BackgroundThe standardization of biological data using unique identifiers is vital for seamless data integration, comprehensive interpretation, and reproducibility of research findings, contributing to advancements in bioinformatics and systems biology. Despite being widely accepted as a universal identifier, scientific names for biological species have inherent limitations, including lack of stability, uniqueness, and convertibility, hindering their effective use as identifiers in databases, particularly in natural product (NP) occurrence databases, posing a substantial obstacle to utilizing this valuable data for large-scale research applications.ResultTo address these challenges and facilitate high-throughput analysis of biological data involving scientific names, we developed PhyloSophos, a Python package that considers the properties of scientific names and taxonomic systems to accurately map name inputs to entries within a chosen reference database. We illustrate the importance of assessing multiple taxonomic databases and considering taxonomic syntax-based pre-processing using NP occurrence databases as an example, with the ultimate goal of integrating heterogeneous information into a single, unified dataset.ConclusionsWe anticipate PhyloSophos to significantly aid in the systematic processing of poorly digitized and curated biological data, such as biodiversity information and ethnopharmacological resources, enabling full-scale bioinformatics analysis using these valuable data resources.

The importance of taxonomy for determining species distribution: a case study using the disjunct lichen Brodoa oroarctica

Species-focused conservation requires a thorough understanding of species’ distributions. Delineating a species’ distribution requires taxonomic knowledge and adequate occurrence data. For plants and fungi, herbaria represent a valuable source of large-scale occurrence data. Advances in digital technology mean that data from many herbarium collections worldwide are now easily accessible. However, species concepts can change over time requiring herbarium records to be re-examined and databases updated, which does not always occur synchronously across all collections. Therefore, non-critical use of these data can promote inaccuracies in understanding species distributions. Taxonomic revisions are common in understudied organisms, such as lichens. Here, we illustrate how changing taxonomy and non-critical acceptance of online data affects our understanding of disjunct distributions, using the lichen Brodoa oroarctica (Krog) Goward as an example. Defining the distribution of the arctic lichen B. oroarctica is confounded by changing taxonomy and uncertainty of herbarium records that pre-date taxonomic revisions. We review the distribution of this species in the literature and in aggregate occurrence databases, and verify herbarium specimens that represent disjunct occurrences in eastern North America to present an updated account of its distribution and frequency in eastern North America. We show that knowledge of changing species taxonomy is essential to depicting accurate species distributions.

A comprehensive database of squirrel distribution and occurrence in South Asia.

The Squirrels of South Asia (SOSA) database compiles comprehensive distribution and occurrence information on all squirrel species that occur in this region (34 species). These 34 squirrel species, including tree, flying and ground squirrels, represent 14% of global sciurid diversity. The database collates curated data from various sources such as museums, literature, primary fieldwork, citizen science and social media platforms and covers the entire distributional ranges of the target species, including countries in Central Asia and Southeast Asia when required. The SOSA database enhances our understanding of squirrel distribution, population dynamics and their conservation needs in South Asia by consolidating information. It aims to be a valuable resource for researchers, conservationists and wildlife enthusiasts. As of March 2023, the database comprises over 40,000 records of 34 species in over 30 countries globally. Spending an average of 334 hours on each species, more than 20 data collectors put in over 10,000 hours to gather, curate and build this database. The database has resulted in novel records of species occurrence in regions and countries that are poorly represented in currently available global data repositories. The current version which has been made public via GBIF comprises of 1187 records of all 34 species across multiple sources. This is a subset of the SOSA database.

GlobalAMFungi: a global database of arbuscular mycorrhizal fungal occurrences from high-throughput sequencing metabarcoding studies.

Arbuscular mycorrhizal (AM) fungi are crucial mutualistic symbionts of the majority of plant species, with essential roles in plant nutrient uptake and stress mitigation. The importance of AM fungi in ecosystems contrasts with our limited understanding of the patterns of AM fungal biogeography and the environmental factors that drive those patterns. This article presents a release of a newly developed global AM fungal dataset (GlobalAMFungi database, https://globalamfungi.com) that aims to reduce this knowledge gap. It contains almost 50 million observations of Glomeromycotinian AM fungal amplicon DNA sequences across almost 8500 samples with geographical locations and additional metadata obtained from 100 original studies. The GlobalAMFungi database is built on sequencing data originating from AM fungal taxon barcoding regions in: i) the small subunit rRNA (SSU) gene; ii) the internal transcribed spacer 2 (ITS2) region; and iii) the large subunit rRNA (LSU) gene. The GlobalAMFungi database is an open source and open access initiative that compiles the most comprehensive atlas of AM fungal distribution. It is designed as a permanent effort that will be continuously updated by its creators and through the collaboration of the scientific community. This study also documented applicability of the dataset to better understand ecology of AM fungal taxa.

Automated Detection and Tracking of Equatorial Plasma Bubbles Utilizing Global‐Scale Observations of the Limb and Disk (GOLD) 135.6 nm Data

AbstractEquatorial plasma bubbles (EPBs) are regions of depleted plasma within the ionosphere that form during post‐sunset hours near the magnetic equator. EPBs tend to align with local geomagnetic field lines, extend hundreds of kilometers along geomagnetic longitudes, and thousands of kilometers along geomagnetic latitudes. EPBs can attenuate lower frequency radio waves, such as HF radar. Smaller features, usually 10s of meters, along the EPB's wall can interfere with centimeter scale wavelengths, such as GPS, via Bragg scattering. Statistical analysis of EPBs can further understanding of their occurrence and behavior. The current study utilizes Global‐Scale Observations of the Limb and Disk (GOLD) 135.6 nm nightglow data from 5 October 2018 to 30 September 2022. GOLD has a unique perspective from geostationary orbit, allowing consistent viewing of nightglow and structures over the Americas and Atlantic. An EPB detection method is developed and used to generate a database of occurrences. Occurrences are used to calculate EPB drift speeds and separations. All data is looked at as a whole, including any possible solar or geomagnetic disturbance periods. Seasonality in occurrence rate is evident. Occurrences peak during December solstice and minimize during June solstice for longitudes seen by GOLD. Within GOLD's view, higher occurrences are seen to the west during December solstice and to the east during June solstice. EPB drift speeds and separations show consistent distributions regardless of magnetic latitude region, geographic region, or season. This suggests EPBs behave consistently and regularly once formed, at least on spatial scales observed by GOLD.

Melaleuca (Myrtaceae): Biogeography of an important genus of trees and shrubs in a changing world

The number of naturalised and invasive woody plant species has increased rapidly in recent decades. Despite the increasing interest in tree and shrub invasions, little is known about the invasion ecology of most species. This paper explores the global movement of species in the genus Melaleuca (Myrtaceae; here including the genus Callistemon). We assess the global introduction history, distribution and biogeographic status of the genus. Various global species occurrence databases, citizen science (iNaturalist), and the literature were used.Seventy-two species [out of 386 Melaleuca species; 19%] have been introduced to at least 125 regions outside their native range. The main regions of global Melaleuca introductions are Southeast Asia, the southern parts of North America, south-eastern South America, southern Africa and Europe. The earliest record of a Melaleuca species outside of the native range of the genus is 1789. First records of Melaleuca species outside their native range were most commonly recorded in the 1960s, with records from all over the world. The main reasons for Melaleuca introductions were for use in the tea tree (pharmaceutical value) and ornamental horticulture industries. Melaleuca introductions, naturalizations and invasions are recent compared to many other woody plant taxa. Experiences in Florida and South Africa highlight the potential of Melaleuca species to spread rapidly and have significant ecological impacts. It is likely that the accumulating invasion debt will result in further naturalization and invasion of Melaleuca species in the future.