scholarly journals GAPeDNA: Assessing and mapping global species gaps in genetic databases for metabarcoding studies

2021 ◽  
Vol 4 ◽  
Author(s):  
Virginie Marques ◽  
Tristan Milhau ◽  
Camille Albouy ◽  
Tony Dejean ◽  
Stéphanie Manel ◽  
...  
Keyword(s):  
Threatened Species ◽  
Large Scale ◽  
Conservation Status ◽  
Environmental Dna ◽  
Bulk Sample ◽  
Data Availability ◽  
Reference Database ◽  
Flexible Tool ◽  
Initial Application ◽  
Wide Range

Environmental DNA metabarcoding has recently emerged as a non-invasive tool for aquatic biodiversity inventories, frequently surpassing traditional methods for detecting a wide range of taxa in most habitats. One of the major limitations currently impairing the large-scale application of DNA-based inventories, such as eDNA or bulk-sample analysis is the lack of species sequences available in public genetic databases. These gaps are still largely unknown spatially and taxonomically for most regions of the world, which can hinder targeted future sequencing efforts. We propose GAPeDNA, a user-friendly web-interface (Fig. 1) that provides a global overview of genetic database completeness for a given taxon across space and conservation status. As an initial application, we synthetized data from regional checklists for marine and freshwater fishes along with their IUCN conservation status to provide global maps of species coverage using the European Nucleotide Archive public reference database for 19 metabarcoding primers. This tool automatizes the scanning of gaps in these databases to guide future sequencing efforts and support the deployment of DNA-based inventories at larger scale. It is flexible and can be expanded to other taxa and primers upon data availability. Using our global fish case study, we show that gaps increase toward the tropics where species diversity and the number of threatened species were the highest. It highlights priority areas for fish sequencing like the Congo, the Mekong and the Mississippi freshwater basins which host more than 60 non-sequenced threatened fish species. For marine fishes, the Caribbean and East Africa host up to 42 non-sequenced threatened species. As an open-acces, updatable and flexible tool, GAPeDNA can be used to evaluate the completeness of sequence reference libraries of various markers and for any taxonomic group.

scholarly journals A large-scale ecological assessment of Swiss rivers using environmental DNA for the monitoring of macroinvertebrates 

2021 ◽  
Vol 4 ◽  
Author(s):  
Jeanine Brantschen ◽  
Rosetta Blackman ◽  
Jean-Claude Walser ◽  
Florian Altermatt
Keyword(s):  
Random Forest ◽  
Community Composition ◽  
Large Scale ◽  
Anthropogenic Activities ◽  
Ecological Status ◽  
Environmental Dna ◽  
Biotic Index ◽  
Reference Database ◽  
Macroinvertebrate Communities ◽  
Monitoring Methods

Anthropogenic activities are changing the state of ecosystems worldwide, affecting community composition and often resulting in loss of biodiversity. Riverine ecosystems are among the most impacted ecosystems. Recording their current state with regular biomonitoring is important to assess the future trajectory of biodiversity. However, traditional monitoring methods for ecological assessments are costly and time-intense. Here, we compare environmental DNA (eDNA) to traditional kick-net sampling in a standardized framework of surface water quality assessment. We use surveys of macroinvertebrate communities to assess biodiversity and the biological state of riverine systems. Both methods were employed to monitor aquatic macroinvertebrate indicator groups at 92 sites across major Swiss river catchments. The eDNA data were taxonomically assigned using a customised reference database. All zero-radius Operational Taxonomic Units (zOTUs) mapping to one of the 142 traditionally used indicator taxon levels were used for subsequent diversity analyses (n = 205). At the site level, eDNA detected less indicator taxa than the kick-net method and alpha diversity correlated only weakly between the methods. However, the methods showed a strong congruence in the overall community composition (gamma diversity), as the same indicator groups were commonly detected. In order to set the community composition in relation to the biotic index, the ecological states of the sampling sites were predicted by a random forest approach. Using all zOTUs mapping to macroinvertebrate indicator groups (n = 693) as predictive features, the random forest models successfully predicted the ecological status of the sampled sites. The majority of the predictions (71%) resulted in the same classification like the kick-net based scores. Thus, the sampling of eDNA enabled the detection of indicator communities and provided valuable classifications of the ecological state, when combined with machine learning. Overall, eDNA based sampling has the potential to complement traditional surveys of macroinvertebrate communities in routine large-scale assessments in a non-invasive and scalable approach.

Water-balance response to climate variability, a small-to-large scale Italian dataset

2021 ◽  
Author(s):  
Giulia Bruno ◽  
Francesco Avanzi ◽  
Simone Gabellani ◽  
Luca Ferraris ◽  
Edoardo Cremonese ◽  
...  
Keyword(s):  
Water Balance ◽  
Water Resource Management ◽  
Large Scale ◽  
Hydrological Cycle ◽  
Climatic Variability ◽  
Remote Sensing Data ◽  
Data Availability ◽  
Catchment Scale ◽  
Wide Range ◽  
Mean Square Errors

<p>Understanding how deficit of precipitation impacts the hydrological cycle is of growing interest and is essential for water resource management. It has been recently observed that the relationship between precipitation and runoff during droughts is subjected to a shift in the sense that the predicted runoff is much less than the one expected due to the deficit in precipitation. Unraveling why this occurs requires an accurate knowledge of all the components of the water balance equation. However, large-scale and consistent samples of precipitation, runoff, evapotranspiration, ET and change in storage have always been challenging to collect. Here, we hypothesized that blending ground-based and remote-sensing data products could fill this gap. We present a countrywide dataset of catchment-scale water balance, covering the last 10 water years in Italy. Italy shows a broad variety of climatic and topographic features and faced several droughts over recent years. We use ground-based daily runoff data, interpolated precipitation maps, and a remote-sensed daily evapotranspiration dataset from the LSASAF ET product. The ET dataset is additionally compared with flux towers data across the country, obtaining root mean square errors on the order of 30 mm/month. Lastly, changes in storage are estimated to close the water balance. More than 100 catchments - including the major Italian basins - are selected, according to data availability and reliability. These catchments cover a wide range of size, morphologic and climatic characteristics. </p><p>This dataset is a strategic source of information to analyze catchment-scale runoff, ET and storage response to climatic variability across climates and landscapes.</p>

scholarly journals Distribution and conservation status of fairy shrimps (Crustacea: Anostraca) in the astatic soda pans of the Carpathian basin: the role of local and spatial factors

2013 ◽  
Vol 72 (1) ◽  
pp. 9 ◽  
Author(s):  
Zsófia Horváth ◽  
Csaba Ferenc Vad ◽  
Lajos Vörös ◽  
Emil Boros
Keyword(s):  
Land Use ◽  
Large Scale ◽  
Conservation Status ◽  
Carpathian Basin ◽  
Suitable Habitat ◽  
Spatial Effects ◽  
High Preference ◽  
Wide Range ◽  
Habitat Generalist

The distribution of Branchinecta orientalis, B. ferox and Chirocephalus carnuntanus was assessed in the natural and semi-natural astatic soda pans of the Carpathian basin. In Europe, these habitats are exclusively restricted to Hungary (Great Hungarian Plain), Austria (Seewinkel) and Serbia (Vojvodina). The present research is the first comprehensive large-scale study – covering an area of approximately 125,000 km2 – on these three fairy shrimp species in the region, and it is important especially in the case of Branchinecta spp., due to former taxonomical uncertainties. The local, land use and spatial effects on the species distribution were also analysed. The three anostracans were found to adopt different strategies, mainly according to the salinity of the pans. The apparently halophilous B. orientalis tolerated higher salinities than the other species, which can be regarded as habitat-generalist halotolerants, showing a high preference for soda waters in Central Europe. The density of the species was significantly affected only by local factors, while their occurrence was influenced also by pan isolation. Land use did not explain a significant amount of variation in either case. In conclusion, soda pans with a wide range of different salinities constitute a suitable habitat for all the three species. Also, protected areas with high number of pans – as Seewinkel (in Austria) or Kiskunság (in Hungary) – can play an essential role in the long-term conservation of these anostracans. Finally, we suggest that these species should be legally protected, primarily because the number of their habitats in the basin is seriously declining.

scholarly journals Towards the extended barcode concept: Generating DNA reference data through genome skimming of danish plants

2021 ◽  
Author(s):  
Physilia Y.S Chua ◽  
Frederik Leerhoi ◽  
Emilia M.R Langkjaer ◽  
Ashot Margaryan ◽  
Christina L Noer ◽  
...  
Keyword(s):  
Reference Data ◽  
Gc Content ◽  
Environmental Dna ◽  
Nuclear Ribosomal Dna ◽  
Reference Database ◽  
Dna Yield ◽  
Chloroplast Genomes ◽  
Wide Range ◽  
Genome Skimming ◽  
Taxonomic Assignments

Recently, there has been a push towards the extended barcode concept of utilising chloroplast genomes (cpGenome) and nuclear ribosomal DNA (nrDNA) sequences for molecular identification of plants instead of the standard barcode regions. These extended barcodes has a wide range of applications, including biodiversity monitoring and assessment, primer design, and evolutionary studies. However, these extended barcodes are not well represented in global reference databases. To fill this gap, we generated cpGenomes and nrDNA reference data from genome skims of 184 plant species collected in Denmark. We further explored the application of our generated reference data for molecular identifications of plants in an environmental DNA metagenomics study. We assembled partial cpGenomes for 82.1% of sequenced species and full or partial nrDNA sequences for 83.7% of species. We added all assemblies to GenBank, of which chloroplast reference data from 101 species and nuclear reference data from 6 species were not previously represented. On average, we recovered 45 genes per species. The rate of recovery of standard barcodes was higher for nuclear barcodes (>89%) than chloroplast barcodes (< 60%). Extracted DNA yield did not affect assembly outcome, whereas high GC content did so negatively. For the in silico simulation of metagenomic reads, taxonomic assignments using the reference data generated had better species resolution (94.9%) as compared to GenBank (18.1%) without any identification errors. Genome skimming generates reference data of both standard barcodes and other loci, contributing to the global DNA reference database for plants.

scholarly journals Airborne environmental DNA for terrestrial vertebrate community monitoring

2021 ◽  
Author(s):  
Christina Lynggaard ◽  
Mads Frost Bertelsen ◽  
Casper V. Jensen ◽  
Matthew S. Johnson ◽  
Tobias Guldberg Froslev ◽  
...  
Keyword(s):  
Large Scale ◽  
Environmental Dna ◽  
Cost Effective ◽  
Monitoring Methods ◽  
Natural Ecosystems ◽  
Terrestrial Vertebrate ◽  
Detection Failure ◽  
Routine Monitoring ◽  
Community Monitoring ◽  
Wide Range

Assessing and studying the distribution, ecology, diversity and movements of species is key in understanding environmental and anthropogenic effects on natural ecosystems. Although environmental DNA is rapidly becoming the tool of choice to assess biodiversity there are few eDNA sample types that effectively capture terrestrial vertebrate diversity and those that do can be laborious to collect, require special permits and contain PCR inhibitory substances, which can lead to detection failure. Thus there is an urgent need for novel environmental DNA approaches for efficient and cost-effective large-scale routine monitoring of terrestrial vertebrate diversity. Here we show that DNA metabarcoding of airborne environmental DNA filtered from air can be used to detect a wide range of local vertebrate taxa. We filtered air at three localities in Copenhagen Zoo, detecting mammal, bird, amphibian and reptile species present in the zoo or its immediate surroundings. Our study demonstrates that airDNA has the capacity to complement and extend existing terrestrial vertebrate monitoring methods and could form the cornerstone of programs to assess and monitor terrestrial communities, for example in future global next generation biomonitoring frameworks.

scholarly journals Population trends and status of the Madeira Laurel Pigeon Columba trocaz

1999 ◽  
Vol 9 (4) ◽  
pp. 387-395 ◽  
Author(s):  
Paulo Oliveira ◽  
Martin Jones ◽  
Donato Caires ◽  
Dilia Menezes
Keyword(s):  
Population Density ◽  
Threatened Species ◽  
Large Scale ◽  
Considerable Increase ◽  
Sampling Methods ◽  
Conservation Status ◽  
Distance Sampling ◽  
Population Changes ◽  
Laurel Forest ◽  
Large Scale Survey

SummaryA survey was undertaken in 1995 to assess the conservation status of the Madeira Laurel Pigeon Columba trocaz, a threatened species endemic to the Island of Madeira. The first large scale survey was carried out 1986, following the cessation of legal hunting of the species, to provide a baseline for future monitoring of population changes. The current study therefore aims to (1) compare population size with those of 1986 and (2) employ distance sampling methods (not used in 1986) to obtain estimates of population density and size. Eighteen transects (13 repeated from the 1986 survey and five new) were conducted in the four main areas of laurel forest. Pigeon numbers had increased on nearly all transects but some of the highest increases, proportionately and often numerically, were in areas with lower numbers in 1986. We estimate the current population to be 10,400 individuals, a considerable increase since 1986, probably due to a ban on hunting. As laurel forest habitat is now very well protected the Madeira Laurel Pigeon is relatively safe from extinction.

Electron microscopy study of reactively sputter-deposited Ti/N films on silicon

1992 ◽  
Vol 50 (2) ◽  
pp. 1362-1363
Author(s):  
V. C. Kannan ◽  
A. K. Singh ◽  
R. B. Irwin ◽  
S. Chittipeddi ◽  
F. D. Nkansah ◽  
...  
Keyword(s):  
Integrated Circuits ◽  
Large Scale ◽  
Hexagonal Phase ◽  
Microscopy Study ◽  
Electron Microscopy Study ◽  
Process Conditions ◽  
Tin Films ◽  
Wide Range ◽  
Fcc Phase ◽  
Circuits Vlsi

Titanium nitride (TiN) films have historically been used as diffusion barrier between silicon and aluminum, as an adhesion layer for tungsten deposition and as an interconnect material etc. Recently, the role of TiN films as contact barriers in very large scale silicon integrated circuits (VLSI) has been extensively studied. TiN films have resistivities on the order of 20μ Ω-cm which is much lower than that of titanium (nearly 66μ Ω-cm). Deposited TiN films show resistivities which vary from 20 to 100μ Ω-cm depending upon the type of deposition and process conditions. TiNx is known to have a NaCl type crystal structure for a wide range of compositions. Change in color from metallic luster to gold reflects the stabilization of the TiNx (FCC) phase over the close packed Ti(N) hexagonal phase. It was found that TiN (1:1) ideal composition with the FCC (NaCl-type) structure gives the best electrical property.

THE SOME QUESTIONS OF AUTONOMOUS MOTION AND MANAGEMENT OF LAND-MOBILE ROBOTIC COMPLEXES FOR UKRAINIAN GROUND FORCESE

2019 ◽  
pp. 53-58
Author(s):  
О. Кravchuk ◽  
V. Symonenkov ◽  
I. Symonenkova ◽  
O. Hryhorev
Keyword(s):  
Large Scale ◽  
Armed Forces ◽  
Distributed Information ◽  
Wide Range ◽  
Highly Effective ◽  
Information Management Systems ◽  
Robotic Devices ◽  
Principles And Standards ◽  
And Control ◽  
The Eu

Today, more than forty countries of the world are engaged in the development of military-purpose robots. A number of unique mobile robots with a wide range of capabilities are already being used by combat and intelligence units of the Armed forces of the developed world countries to conduct battlefield intelligence and support tactical groups. At present, the issue of using the latest information technology in the field of military robotics is thoroughly investigated, and the creation of highly effective information management systems in the land-mobile robotic complexes has acquired a new phase associated with the use of distributed information and sensory systems and consists in the transition from application of separate sensors and devices to the construction of modular information subsystems, which provide the availability of various data sources and complex methods of information processing. The purpose of the article is to investigate the ways to increase the autonomy of the land-mobile robotic complexes using in a non-deterministic conditions of modern combat. Relevance of researches is connected with the necessity of creation of highly effective information and control systems in the perspective robotic means for the needs of Land Forces of Ukraine. The development of the Armed Forces of Ukraine management system based on the criteria adopted by the EU and NATO member states is one of the main directions of increasing the effectiveness of the use of forces (forces), which involves achieving the principles and standards necessary for Ukraine to become a member of the EU and NATO. The inherent features of achieving these criteria will be the transition to a reduction of tasks of the combined-arms units and the large-scale use of high-precision weapons and land remote-controlled robotic devices. According to the views of the leading specialists in the field of robotics, the automation of information subsystems and components of the land-mobile robotic complexes can increase safety, reliability, error-tolerance and the effectiveness of the use of robotic means by standardizing the necessary actions with minimal human intervention, that is, a significant increase in the autonomy of the land-mobile robotic complexes for the needs of Land Forces of Ukraine.

Stirring and aeration system for the upgrading of small waste water treatment plants

1994 ◽  
Vol 29 (12) ◽  
pp. 149-156 ◽  
Author(s):  
Marcus Höfken ◽  
Katharina Zähringer ◽  
Franz Bischof
Keyword(s):  
Waste Water ◽  
Water Treatment ◽  
Large Scale ◽  
Waste Water Treatment ◽  
Water Treatment Plants ◽  
Waste Water Treatment Plants ◽  
Basic Fluid ◽  
Aeration System ◽  
Technical Realization ◽  
Wide Range

A novel agitating system has been developed which allows for individual or combined operation of stirring and aeration processes. Basic fluid mechanical considerations led to the innovative hyperboloid design of the stirrer body, which ensures high efficiencies in the stirring and the aeration mode, gentle circulation with low shear forces, excellent controllability, and a wide range of applications. This paper presents the basic considerations which led to the operating principle, the technical realization of the system and experimental results in a large-scale plant. The characteristics of the system and the differences to other stirring and aeration systems are illustrated. Details of the technical realization are shown, which conform to the specific demands of applications in the biological treatment of waste water. Special regard is given to applications in the upgrading of small compact waste water treatment plants.

Thin structure of heterogeneous and multiphase fluid flows

2012 ◽  
Vol 9 (1) ◽  
pp. 175-180
Author(s):  
Yu.D. Chashechkin
Keyword(s):  
Large Scale ◽  
Fundamental System ◽  
Fluid Flows ◽  
Regular Solutions ◽  
Flow Models ◽  
Group Methods ◽  
Wide Range ◽  
Thin Structure ◽  
Multiphase Fluid ◽  
Complete Solutions

According to the results of visualization of streams, the existence of structures in a wide range of scales is noted: from galactic to micron. The use of a fundamental system of equations is substantiated based on the results of comparing symmetries of various flow models with the usage of theoretical group methods. Complete solutions of the system are found by the methods of the singular perturbations theory with a condition of compatibility, which determines the characteristic equation. A comparison of complete solutions with experimental data shows that regular solutions characterize large-scale components of the flow, a rich family of singular solutions describes formation of the thin media structure. Examples of calculations and observations of stratified, rotating and multiphase media are given. The requirements for the technique of an adequate experiment are discussed.

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