scholarly journals (e)DNA-based assessments within one of the World's largest river survey programs: summarized insights from the 4th Joint Danube Survey

2021 ◽  
Vol 4 ◽  
Author(s):  
Alexander Weigand
Keyword(s):  
Genetic Diversity ◽  
Large Scale ◽  
State Of The Art ◽  
Dna Barcode ◽  
Ecological Status ◽  
Environmental Dna ◽  
Species Level ◽  
Molecular Tools ◽  
Spatiotemporal Changes ◽  
And Training

With the 4th Joint Danube Survey in 2019 (JDS4), for the first time, DNA- and environmental DNA-based approaches were integrated into the program of the JDS, focussing on the three biological quality elements of fish, macrozoobenthos and phytobenthos, and additionally on the sediment community (Liska et al. 2021, Weigand and Astrin 2021). The rationals for including (e)DNA-based tools into the survey's program were that i) many hard-to-identify organism groups can be assessed down to their species level, ii) taxonomic information can be unlocked even in cases where morphotaxonomic knowledge and expertise are limited, iii) all developmental stages, cryptic species and indeterminable sexes can be potentially identified, iv) taxalists relying on sequence-based information are reproducible and comparable in space and time (aspects, which are particularly important for a longitudinal survey involving many countries), and, v) this additional line of taxonomic evidence will help to draw a more precise and comprehensive picture of the Danubian biota. The target groups were assessed using group-specific (e)DNA-based metabarcoding approaches (for fish: Pont et al. 2021; macrozoobenthos: Beermann et al. 2021; phytobenthos: Zimmermann et al. 2021; sediment community: Cordier et al. 2021). The coverage of barcode libraries for Danubian biota were checked prior to conducting the metabarcoding approaches. Coverage values based on JDS3 outcomes were >90% for fish (12S, but depending on reference database), 84% for macrozoobenthos (COI) and 69% and 88% for all, respectively, only abundant phytobenthos species (18S + rbcL), so that (e)DNA-based approaches were expected to be implemented effectively from this perspective (Weigand and Astrin 2021). Although still a certain degree of methodological variation exists, the outcomes clearly demonstrate the huge potential of (e)DNA-based approaches for complementary biodiversity and ecological status class assessments: eDNA water analysis of fish revealed most of the taxa also detected by the traditional fish survey, but was particularly effective in detecting hard-to-capture benthic taxa (including endangered sturgeon species) and fish traces originating from waste water treatment plants (Pont et al. 2021). Many of the traditionally assigned macrozoobenthos species were detected by DNA metabarcoding as well, but sequence data allowed to add a plethora of new chironomid and oligochaete species to the taxalist. Molecular ecological status class assessments based on presence-absence values of macrozoobenthos species were largely congruent to traditional abundance or presence-absence-based outcomes (Beermann et al. 2021, Weigand 2021). Although traditional light microscopy, which is based on identifying phytobenthos species by their frostules, revealed a higher number of diatom species, the molecular assessment detected much more taxa (i.e. MOTUs), which await species-level taxonomic annotation in the future (Zimmermann et al. 2021). Metabarcoding of the sediment community was particularly effective to assess meiofaunal species and allowed the molecular inference of fine sediment quality based on local community structures of vulnerable nematode species (Cordier et al. 2021). Finally, all (e)DNA-based taxalists were compiled to inform invasive alien species detection in the Danube River Basin. However, despite their promising performance and large coherence with traditional outcomes during JDS4, the full potential of (e)DNA-based approaches in the context of larger environmental surveys might be further released by developing and curating catchment-specific DNA barcode reference libraries, focussing on a small(er) set of standardized (e)DNA-based approaches, integrating genetic diversity (and spatiotemporal changes thereof) in ecological status class assessments, installing a dense, large-scale environmental DNA-based screening, based on which traditional surveys can be performed at conspicuous sites, and, educating and training national authorities in state-of-the-art molecular tools. developing and curating catchment-specific DNA barcode reference libraries, focussing on a small(er) set of standardized (e)DNA-based approaches, integrating genetic diversity (and spatiotemporal changes thereof) in ecological status class assessments, installing a dense, large-scale environmental DNA-based screening, based on which traditional surveys can be performed at conspicuous sites, and, educating and training national authorities in state-of-the-art molecular tools. Already today, (e)DNA-based methods can be seen as an effective and complementary tool to provide consolidated results for biodiversity and ecological status class assessments in a highly integrative and international setup, as pursued during JDS4.

scholarly journals Relieving the Incompatibility of Network Representation and Classification for Long-Tailed Data Distribution

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Hao Hu ◽  
Mengya Gao ◽  
Mingsheng Wu
Keyword(s):  
Large Scale ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Data Distribution ◽  
Distribution Problem ◽  
Imbalanced Dataset ◽  
Network Representation ◽  
Knowledge Distillation ◽  
Rare Classes ◽  
And Training

In the real-world scenario, data often have a long-tailed distribution and training deep neural networks on such an imbalanced dataset has become a great challenge. The main problem caused by a long-tailed data distribution is that common classes will dominate the training results and achieve a very low accuracy on the rare classes. Recent work focuses on improving the network representation ability to overcome the long-tailed problem, while it always ignores adapting the network classifier to a long-tailed case, which will cause the “incompatibility” problem of network representation and network classifier. In this paper, we use knowledge distillation to solve the long-tailed data distribution problem and fully optimize the network representation and classifier simultaneously. We propose multiexperts knowledge distillation with class-balanced sampling to jointly learn high-quality network representation and classifier. Also, a channel activation-based knowledge distillation method is also proposed to improve the performance further. State-of-the-art performance on several large-scale long-tailed classification datasets shows the superior generalization of our method.

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.

scholarly journals Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population

2019 ◽  
Author(s):  
Satsuki Tsuji ◽  
Atsushi Maruyama ◽  
Masaki Miya ◽  
Masayuki Ushio ◽  
Hirotoshi Sato ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Water Sample ◽  
Sanger Sequencing ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Dna Analysis ◽  
Environmental Dna ◽  
Intraspecific Diversity ◽  
Survey Method ◽  
Intraspecific Genetic Diversity

AbstractEnvironmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA-based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish (Plecoglossus altivelis altivelis) detected in a capture survey could also be detected from an eDNA sample derived from the field that contained various haplotypes with low concentrations and foreign substances. A water sample and Ayu specimens collected from a river on the same day were analysed by eDNA analysis and Sanger sequencing, respectively. The 10 L water sample was divided into 20 filters for each of which 15 PCR replications were performed. After high-throughput sequencing, denoising was performed using two of the most widely used denoising packages, UNOISE3 and DADA2. Of the 42 haplotypes obtained from the Sanger sequencing of 96 specimens, 38 (UNOISE3) and 41 (DADA2) haplotypes were detected by eDNA analysis. When DADA2 was used, except for one haplotype, haplotypes owned by at least two specimens were detected from all the filter replications. This study showed that the eDNA analysis for evaluating intraspecific genetic diversity provides comparable results for large-scale capture-based conventional methods, suggesting that it could become a more efficient survey method for investigating intraspecific genetic diversity in the field.

scholarly journals Applicability of DNA-based identifications for the WFD-guided monitoring using macroinvertebrates: a large-scale DNA metabarcoding study for implementing routine ecological status assessments in Iberian rivers

2021 ◽  
Vol 4 ◽  
Author(s):  
Raquel González ◽  
Juan Antonio Villaescusa ◽  
Antonio Picazo ◽  
Ana M. Pujante ◽  
Antonio Camacho
Keyword(s):  
Large Scale ◽  
Mitochondrial Gene ◽  
Dna Barcode ◽  
Ecological Status ◽  
Pcr Amplification ◽  
Taxonomic Composition ◽  
Amplification Bias ◽  
Dna Metabarcoding ◽  
Physical And Chemical Variables ◽  
Iberian Rivers

Over the last decade, remarkable improvements have been made in the field of metabarcoding-based tools for routine ecological status assessments. However, important issues are yet to be solved to fulfil the European Water Framework Directive (WFD) requirements and standards. These limitations, which include problems related to e.g. the lack of a complete COI macroinvertebrate barcode database available for the Iberian Peninsula Murria 2020, or the scarce recovery of specific taxa due to DNA extraction and/or PCR amplification bias, are especially difficult to overcome for routine freshwater macroinvertebrate monitoring. For that purpose, a large-scale study is on going to test how metabarcoding data can infer existing macroinvertebrate morphotaxonomy-based biotic indexes and ecological status of Iberian rivers. Freshwater macroinvertebrates were selected as a Biological Quality Element and identified by using both morphological and metabarcoding approaches. The mitochondrial gene for cytochrome c oxidase subunit I (COI) was used as a DNA Barcode. Taxonomic coverage, taxonomic composition metrics and ecological status obtained from both approaches were analysed. Physical and chemical variables obtained during the routine biomonitoring, as well as other ecological parameters including biodiversity indexes, were also assessed. Multivariate data analysis of these environmental and biotic data obtained from both approaches were compared. Results seem to support the hypothesis Kuntke 2019 that the DNA-metabarcoding approach might deliver similar quality assessments results to the morphological approach, though some refinement must be done at the different steps of the process prior to establish a reliable procedure allowing the alternative use of both methods giving similar results for the ecological status classes marked by the WFD.

scholarly journals Intraspecific population admixture of a top piscivore correlates with anthropogenic alteration of freshwater ecosystems

2019 ◽  
Author(s):  
Erik Eschbach ◽  
Arne Wolfram Nolte ◽  
Klaus Kohlmann ◽  
Josep Alos ◽  
Sandro Schöning ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Large Scale ◽  
Environmental Changes ◽  
Ecological Status ◽  
Freshwater Ecosystems ◽  
Genetic Admixture ◽  
Freshwater Biodiversity ◽  
Policy Objective ◽  
Complete Replacement ◽  
Intraspecific Genetic Diversity

AbstractConservation of local genetic diversity is an important policy objective, but intraspecific genetic diversity can be transformed by natural ecological processes associated with anthropogenic changes in ecosystems. Environmental changes and a strong interconnection of drainage systems impact freshwater biodiversity from gene to population level. Populations can either become extinct or expand their range and accompanying secondary contacts can lead to genetic admixture. We investigated how the genetic population structure and the patterns of genetic admixture of Esox lucius L. (the northern pike) vary with the type of ecosystem and the integrity of the ecosystem assessed by measures under the European Water Framework Directive. The pike inhabits river, lake and brackish water ecosystems, where it is confronted with different ecological disturbances. We analysed 1,384 pike samples from the North, Baltic and Black Sea drainages and differentiated between metapopulations from each hydrogeographic region using genotypes from 15 microsatellites and mitochondrial cyt b sequences. Individual populations showed signs of genetic admixture ranging from almost zero to complete replacement by foreign genotypes. Hierarchical general linear modeling revealed a highly significant positive association of the degree of genetic admixture with decreasing ecological status. This may mean that populations in disturbed environments are more prone to influences by foreign genotypes or, alternatively, increased genetic admixture may indicate adaptation to rapid environmental changes. Regardless of the underlying mechanisms, our results suggest that anthropogenic alterations of natural freshwater ecosystems can influence genetic structures, which may lead to a large-scale reduction of intraspecific genetic diversity.

scholarly journals How many Non-Indigenous Species occurring in the Mediterranean Sea can actually be identified through environmental DNA? A gap analysis of NIS DNA barcodes in the reference libraries

2021 ◽  
Vol 4 ◽  
Author(s):  
Maurizio Pinna ◽  
Francesco Zangaro ◽  
Eftychia Tzafesta ◽  
Valeria Specchia
Keyword(s):  
Alien Species ◽  
Mediterranean Sea ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Indigenous Species ◽  
Dna Barcodes ◽  
Molecular Tools ◽  
Amplification Process ◽  
The Mediterranean ◽  
Non Indigenous Species

The Mediterranean Sea is known for hosting a high diversity of species, with more than 17,000 reported marine species, one fifth which are endemic. Moreover, the number of non-indigenous species (NIS) in the Mediterranean Sea is recently reported to be increasing. The monitoring and the distribution of NIS is a key requirement for the conservation and management of the ecosystems, as also foreseen by the regulation (EU) No 1143/2014 of the European Parliament and of the Council of 22 October 2014 on the prevention and management of the introduction and spread of invasive alien species. A promising innovative approach for the identification of species and biodiversity is the use of molecular tools (DNA barcoding and metabarcoding). Combined with environmental DNA (eDNA) extracted from environmental samples like water or sediment, traces of species can be identified. Currently, the main limitation in the use of molecular tools (DNA barcoding and metabarcoding, eDNA) for species identification is the incompleteness of the DNA barcode reference databases. We assessed the extent of gaps in DNA barcode reference libraries, using the most updated inventory of 666 confirmed alien species occurring in the Mediterranean Sea. Also, the availability of primers for the amplification process was investigated. 32.58% of these species lack DNA barcodes in the reference libraries. Also, 70% of the retrieved NIS in the DNA barcode libraries lack the public availability of the primers used for the amplification process. The results of this study allow us to direct scientific efforts towards specific taxonomic groups in order to complete the NIS DNA barcode reference libraries and enable effective application of eDNA in investigations of the occurrence and the distribution of NIS in the Mediterranean Sea, and in the first sighting of still unknown NIS.

scholarly journals Documentary data and the study of past droughts: a global state of the art

2018 ◽  
Vol 14 (12) ◽  
pp. 1915-1960 ◽  
Author(s):  
Rudolf Brázdil ◽  
Andrea Kiss ◽  
Jürg Luterbacher ◽  
David J. Nash ◽  
Ladislava Řezníčková
Keyword(s):  
Large Scale ◽  
State Of The Art ◽  
Drought Indices ◽  
Documentary Evidence ◽  
Climatic Trends ◽  
Instrumental Observations ◽  
Spatio Temporal ◽  
Epigraphic Evidence ◽  
Administrative Evidence

Abstract. The use of documentary evidence to investigate past climatic trends and events has become a recognised approach in recent decades. This contribution presents the state of the art in its application to droughts. The range of documentary evidence is very wide, including general annals, chronicles, memoirs and diaries kept by missionaries, travellers and those specifically interested in the weather; records kept by administrators tasked with keeping accounts and other financial and economic records; legal-administrative evidence; religious sources; letters; songs; newspapers and journals; pictographic evidence; chronograms; epigraphic evidence; early instrumental observations; society commentaries; and compilations and books. These are available from many parts of the world. This variety of documentary information is evaluated with respect to the reconstruction of hydroclimatic conditions (precipitation, drought frequency and drought indices). Documentary-based drought reconstructions are then addressed in terms of long-term spatio-temporal fluctuations, major drought events, relationships with external forcing and large-scale climate drivers, socio-economic impacts and human responses. Documentary-based drought series are also considered from the viewpoint of spatio-temporal variability for certain continents, and their employment together with hydroclimate reconstructions from other proxies (in particular tree rings) is discussed. Finally, conclusions are drawn, and challenges for the future use of documentary evidence in the study of droughts are presented.

scholarly journals VIPPrint: Validating Synthetic Image Detection and Source Linking Methods on a Large Scale Dataset of Printed Documents

2021 ◽  
Vol 7 (3) ◽  
pp. 50
Author(s):  
Anselmo Ferreira ◽  
Ehsan Nowroozi ◽  
Mauro Barni
Keyword(s):  
Large Scale ◽  
State Of The Art ◽  
Child Pornography ◽  
Forensic Analysis ◽  
Synthetic Image ◽  
Image Detection ◽  
Face Images ◽  
Large Scale Dataset ◽  
Scanned Images ◽  
Analysis Of The Images

The possibility of carrying out a meaningful forensic analysis on printed and scanned images plays a major role in many applications. First of all, printed documents are often associated with criminal activities, such as terrorist plans, child pornography, and even fake packages. Additionally, printing and scanning can be used to hide the traces of image manipulation or the synthetic nature of images, since the artifacts commonly found in manipulated and synthetic images are gone after the images are printed and scanned. A problem hindering research in this area is the lack of large scale reference datasets to be used for algorithm development and benchmarking. Motivated by this issue, we present a new dataset composed of a large number of synthetic and natural printed face images. To highlight the difficulties associated with the analysis of the images of the dataset, we carried out an extensive set of experiments comparing several printer attribution methods. We also verified that state-of-the-art methods to distinguish natural and synthetic face images fail when applied to print and scanned images. We envision that the availability of the new dataset and the preliminary experiments we carried out will motivate and facilitate further research in this area.

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