scholarly journals DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

2019 ◽  
Author(s):  
Hannah Weigand ◽  
Arne J. Beermann ◽  
Fedor Čiampor ◽  
Filipe O. Costa ◽  
Zoltán Csabai ◽  
...  
Keyword(s):  
Gap Analysis ◽  
Dna Barcode ◽  
Aquatic Biota ◽  
Data Systems ◽  
Content Quality ◽  
Private Data ◽  
Dna Metabarcoding ◽  
Identification Of Species ◽  
Taxonomic Groups ◽  
Future Work

AbstractEffective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilization of metabarcoding in aquatic biomonitoring.

scholarly journals Mind the gap-analysis! – How complete are DNA barcode reference libraries for monitoring-relevant aquatic species in Europe?

2021 ◽  
Vol 4 ◽  
Author(s):  
Hannah Weigand
Keyword(s):  
Gap Analysis ◽  
General Pattern ◽  
Dna Barcode ◽  
Marine Species ◽  
Biotic Index ◽  
Reference Database ◽  
Data Systems ◽  
Freshwater Macroinvertebrates ◽  
Public Data ◽  
Dna Metabarcoding

Molecular species identification with DNA metabarcoding can potentially accelerate, streamline and standardise biomonitoring routines. Currently, it is tested how this new technique can be implemented for the European Water Framework Directive (WFD) and the European Marine Strategy Framework Directive (MSFD). To connect the results from DNA metabarcoding with the current monitoring routines, an extensive, high-quality DNA barcode reference database is required. Hence, a gap-analysis of the Barcode of Life Data Systems (BOLD) was performed as part of the EU-COST Action DNAqua-Net (Weigand et al. 2019), which was updated in 2021. It aimed to analyse the completeness of BOLD for species on the national WFD monitoring lists and for marine species on the ERMS (European Register of Marine Species) and AMBI (AZTI Marine Biotic Index) lists. The data were supplemented by MitoFish for freshwater fish and Diat.barcode for diatoms. Several thousands of species were included in the gap-analysis, although not all countries currently apply species-level data for all WFD biological quality elements. The barcode coverage of the different taxonomic groups varied strongly, with high levels (> 80%) for fish and freshwater vascular plants, and low levels for diatoms and freshwater plathelminths (< 15%). As a general pattern, species monitored by several countries had a higher coverage compared to those monitored only by a single country. The gap-analysis focused additionally on the availability of metadata (e.g., geographical origin of the specimen or determiner name) for the barcodes. Hence, we analysed if the data were stored public (with access to metadata) or private (without access to metadata) in BOLD or if the data were mined from GenBank (metadata are potentially available but not easy to access). Although public data were stored for many species (43% of freshwater macroinvertebrates and 21% of AMBI marine species), the proportion of species without public metadata was not neglectable (22% of freshwater macroinvertebrates and 22% of AMBI marine species). Another issue that emerged from the gap-analysis was that several deposited barcodes were identified by reverse taxonomy (RT), i.e., specimens were molecularly identified via its DNA barcode and the barcode itself is stored in BOLD with the associated species name. This can be problematic as originally misidentified samples can lead to false RT-identifications, making the data appear more trustworthy than it actually is. For the analysed freshwater macroinvertebrates, 39% of all barcodes and 65% of all public data originated from RT, impacting 11% of all monitored species. As the information about RT is only available for publicly stored data, the real impact of RT might even be higher.

scholarly journals DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

2019 ◽  
Vol 678 ◽  
pp. 499-524 ◽  
Author(s):  
Hannah Weigand ◽  
Arne J. Beermann ◽  
Fedor Čiampor ◽  
Filipe O. Costa ◽  
Zoltán Csabai ◽  
...  
Keyword(s):  
Gap Analysis ◽  
Dna Barcode ◽  
Aquatic Biota ◽  
Future Work

scholarly journals Gap analysis for DNA barcodes of aquatic macroinvertebrate species in the Southeast of Italy

2021 ◽  
Vol 4 ◽  
Author(s):  
Valeria Specchia ◽  
Francesco Zangaro ◽  
Eftychia Tzafesta ◽  
Maurizio Pinna
Keyword(s):  
Gap Analysis ◽  
Dna Barcode ◽  
Single Species ◽  
Regional Level ◽  
Dna Barcodes ◽  
Aquatic Macroinvertebrate ◽  
Apulia Region ◽  
Dna Metabarcoding ◽  
Taxonomic Groups ◽  
Macroinvertebrate Species

DNA metabarcoding for the identification of species and ecosystem biomonitoring is a promising innovative approach. The applicability of this tool is at first dependent on the coverage of the DNA sequence reference libraries. We performed a gap analysis of available DNA barcodes in the international databases using the aquatic macroinvertebrate species checklist of the Apulia region in southeast Italy. Our analyses show that 42% of the 1546 examined species do not have representative DNA barcodes in the reference libraries, indicating the importance of working toward their completeness and addressing this effort toward specific taxonomic groups in particular at local/regional level. The DNA-barcode coverage also varies among different taxonomic groups and aquatic ecosystem types in which a large number of species are rare. We also analyzed the DNA barcode reference libraries for the primer set used to barcode species. Only for 52% of the examined barcoded species were the primers reported, indicating the importance of uploading this information in the databases for a more extensive use of the DNA metabarcoding. We also highlighted the opportunity to develop combinations of primers useful at the regional level. We tested the application of the DNA barcoding single species to a lagoon ecosystem (the lagoon named “Aquatina di Frigole” in the Apulia region) which are richer in humic substances than other aquatic environments and in which DNA metabarcoding remains under explored.

scholarly journals Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

NeoBiota ◽  
2021 ◽  
Vol 70 ◽  
pp. 151-165
Author(s):  
Francesco Zangaro ◽  
Benedetta Saccomanno ◽  
Eftychia Tzafesta ◽  
Fabio Bozzeda ◽  
Valeria Specchia ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Special Focus ◽  
Indigenous Species ◽  
Dna Barcodes ◽  
Identification Of Species ◽  
The Mediterranean ◽  
Taxonomic Groups ◽  
Non Indigenous Species

The biodiversity of the Mediterranean Sea is currently threatened by the introduction of Non-Indigenous Species (NIS). Therefore, monitoring the distribution of NIS is of utmost importance to preserve the ecosystems. A promising approach for the identification of species and the assessment of biodiversity is the use of DNA barcoding, as well as DNA and eDNA metabarcoding. Currently, the main limitation in the use of genomic data for species identification is the incompleteness of the DNA barcode databases. In this research, we assessed the availability of DNA barcodes in the main reference libraries for the most updated inventory of 665 confirmed NIS in the Mediterranean Sea, with a special focus on the cytochrome oxidase I (COI) barcode and primers. The results of this study show that there are no barcodes for 33.18% of the species in question, and that 45.30% of the 382 species with COI barcode, have no primers publicly available. This highlights the importance of directing scientific efforts to fill the barcode gap of specific taxonomic groups in order to help in the effective application of the eDNA technique for investigating the occurrence and the distribution of NIS in the Mediterranean Sea.

scholarly journals Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon

2021 ◽  
Author(s):  
Adriana E. Radulovici ◽  
Pedro E. Vieira ◽  
Sofia Duarte ◽  
Marcos A. L. Teixeira ◽  
Luisa M. S. Borges ◽  
...  
Keyword(s):  
Marine Invertebrates ◽  
Dna Barcode ◽  
Current Data ◽  
Data Curation ◽  
Practical Reasons ◽  
Data Systems ◽  
Complex Species ◽  
C Complex ◽  
Taxonomic Groups ◽  
Sequence Quality

AbstractThe accuracy of the identification of unknown specimens using DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. A rampant growth in barcode data led to a stringent need for data curation, especially in taxonomically difficult groups such as marine invertebrates. A major effort in curating marine barcode data deposited in the Barcode of Life Data Systems (BOLD) has been undertaken during the 8th International Barcode of Life Conference (Trondheim, Norway, 2019). For practical reasons, only major taxonomic groups were reviewed and annotated (crustaceans, echinoderms, molluscs, and polychaetes). The congruence of Linnean names with Barcode Index Numbers (BINs) was investigated, and the records deemed uncertain were annotated with four tags: a) MIS-ID (misidentified, mislabeled or contaminated records), b) AMBIG (ambiguous records unresolved with the current data), c) COMPLEX (species occurring in multiple BINs), and d) SHARE (barcodes shared between species). A total of 83,712 specimen records corresponding to 7,576 species were reviewed and 39% of the species were tagged (7% MIS-ID, 17% AMBIG, 14% COMPLEX, and 1% SHARE). High percentages (>50%) of AMBIG tags were recorded in gastropods, whereas COMPLEX tags dominated in crustaceans and polychaetes. This high proportion of tagged species reflects either flaws in the barcoding workflow (e.g., misidentification, cross -contamination) or taxonomic difficulties (e.g., synonyms, undescribed species). Although data curation is crucial for barcode applications, such manual efforts of reviewing large datasets are not sustainable and the implementation of automated solutions to the furthest possible extent is hi ghly desirable.

scholarly journals Gap Analysis for DNA Barcode Reference Libraries for Aquatic Macroinvertebrate Species in the Apulia Region (Southeast of Italy)

2020 ◽  
Vol 8 (7) ◽  
pp. 538
Author(s):  
Valeria Specchia ◽  
Eftychia Tzafesta ◽  
Gabriele Marini ◽  
Salvatore Scarcella ◽  
Simona D’Attis ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Gap Analysis ◽  
Dna Barcode ◽  
Regional Level ◽  
New Combination ◽  
Dna Barcodes ◽  
Aquatic Macroinvertebrate ◽  
Apulia Region ◽  
Taxonomic Groups ◽  
Macroinvertebrate Species

The use of molecular tools (DNA barcoding and metabarcoding) for the identification of species and ecosystem biomonitoring is a promising innovative approach. The effectiveness of these tools is, however, highly dependent on the reliability and coverage of the DNA sequence reference libraries and it also depends on the identification of primer sets that work on the broadest range of taxa. In this study, a gap analysis of available DNA barcodes in the international libraries was conducted using the aquatic macroinvertebrate species checklist of the Apulia region in the southeast of Italy. Our analyses show that 42% of the 1546 examined species do not have representative DNA barcodes in the reference libraries, indicating the importance of working toward their completeness and addressing this effort toward specific taxonomic groups. We also analyzed the DNA barcode reference libraries for the primer set used to barcode species. Only for 52% of the examined barcoded species were the primers reported, indicating the importance of uploading this information in the databases for a more effective DNA barcode implementation effort and extensive use of the metabarcoding method. In this paper, a new combination of primers has revealed its experimental effectiveness at least on the species belonging to the three most represented taxa in the aquatic ecosystems of the Apulia region, highlighting the opportunity to develop combinations of primers useful at the regional level and the importance of studying DNA barcode gaps at the local/regional level. The DNA barcode coverage also varies among different taxonomic groups and aquatic ecosystem types in which a large number of species are rare. We tested the application of the DNA barcoding single species to a lagoon ecosystem (the lagoon named “Acquatina di Frigole” in the Apulia region) and we sampled two macroinvertebrate species lacking DNA barcodes from “Aquatina di Frigole” NATURA 2000 Site IT9150003, Fabulina fabula and Tritia nitida, generated two new CO1 barcodes and added them to a DNA barcode reference library.

scholarly journals Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon

2021 ◽  
Vol 5 ◽  
Author(s):  
Adriana E. Radulovici ◽  
Pedro E. Vieira ◽  
Sofia Duarte ◽  
Marcos A. L. Teixeira ◽  
Luisa M. S. Borges ◽  
...  
Keyword(s):  
Marine Invertebrates ◽  
Dna Barcode ◽  
Data Curation ◽  
Cross Contamination ◽  
Data Systems ◽  
Complex Species ◽  
C Complex ◽  
Taxonomic Groups ◽  
Sequence Quality ◽  
Specimen Identification

The accuracy of specimen identification through DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. The considerable growth in barcode data requires stringent data curation, especially in taxonomically difficult groups such as marine invertebrates. A major effort in curating marine barcode data in the Barcode of Life Data Systems (BOLD) was undertaken during the 8th International Barcode of Life Conference (Trondheim, Norway, 2019). Major taxonomic groups (crustaceans, echinoderms, molluscs, and polychaetes) were reviewed to identify those which had disagreement between Linnaean names and Barcode Index Numbers (BINs). The records with disagreement were annotated with four tags: a) MIS-ID (misidentified, mislabeled, or contaminated records), b) AMBIG (ambiguous records unresolved with the existing data), c) COMPLEX (species names occurring in multiple BINs), and d) SHARE (barcodes shared between species). A total of 83,712 specimen records corresponding to 7,576 species were reviewed and 39% of the species were tagged (7% MIS-ID, 17% AMBIG, 14% COMPLEX, and 1% SHARE). High percentages (>50%) of AMBIG tags were recorded in gastropods, whereas COMPLEX tags dominated in crustaceans and polychaetes. The high proportion of tagged species reflects either flaws in the barcoding workflow (e.g., misidentification, cross-contamination) or taxonomic difficulties (e.g., synonyms, undescribed species). Although data curation is essential for barcode applications, such manual attempts to examine large datasets are unsustainable and automated solutions are extremely desirable.

scholarly journals Predators as Agents of Selection and Diversification

Diversity ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 415
Author(s):  
Jerald B. Johnson ◽  
Mark C. Belk
Keyword(s):  
Natural Selection ◽  
Empirical Evidence ◽  
Mortality Rates ◽  
Predator Species ◽  
Natural Systems ◽  
Evolutionary Diversification ◽  
Multiple Predator Species ◽  
In The Wild ◽  
Taxonomic Groups ◽  
Future Work

Predation is ubiquitous in nature and can be an important component of both ecological and evolutionary interactions. One of the most striking features of predators is how often they cause evolutionary diversification in natural systems. Here, we review several ways that this can occur, exploring empirical evidence and suggesting promising areas for future work. We also introduce several papers recently accepted in Diversity that demonstrate just how important and varied predation can be as an agent of natural selection. We conclude that there is still much to be done in this field, especially in areas where multiple predator species prey upon common prey, in certain taxonomic groups where we still know very little, and in an overall effort to actually quantify mortality rates and the strength of natural selection in the wild.

scholarly journals Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale

2020 ◽  
Vol 8 ◽  
Author(s):  
Zacchaeus G. Compson ◽  
Beverly McClenaghan ◽  
Gregory A. C. Singer ◽  
Nicole A. Fahner ◽  
Mehrdad Hajibabaei
Keyword(s):  
High Throughput Sequencing ◽  
Spatial Scales ◽  
Individual Species ◽  
Biodiversity Assessment ◽  
Occupancy Models ◽  
Widespread Adoption ◽  
Sampling Protocols ◽  
Dna Metabarcoding ◽  
Global Biodiversity ◽  
Taxonomic Groups

Global biodiversity loss is unprecedented, and threats to existing biodiversity are growing. Given pervasive global change, a major challenge facing resource managers is a lack of scalable tools to rapidly and consistently measure Earth's biodiversity. Environmental genomic tools provide some hope in the face of this crisis, and DNA metabarcoding, in particular, is a powerful approach for biodiversity assessment at large spatial scales. However, metabarcoding studies are variable in their taxonomic, temporal, or spatial scope, investigating individual species, specific taxonomic groups, or targeted communities at local or regional scales. With the advent of modern, ultra-high throughput sequencing platforms, conducting deep sequencing metabarcoding surveys with multiple DNA markers will enhance the breadth of biodiversity coverage, enabling comprehensive, rapid bioassessment of all the organisms in a sample. Here, we report on a systematic literature review of 1,563 articles published about DNA metabarcoding and summarize how this approach is rapidly revolutionizing global bioassessment efforts. Specifically, we quantify the stakeholders using DNA metabarcoding, the dominant applications of this technology, and the taxonomic groups assessed in these studies. We show that while DNA metabarcoding has reached global coverage, few studies deliver on its promise of near-comprehensive biodiversity assessment. We then outline how DNA metabarcoding can help us move toward real-time, global bioassessment, illustrating how different stakeholders could benefit from DNA metabarcoding. Next, we address barriers to widespread adoption of DNA metabarcoding, highlighting the need for standardized sampling protocols, experts and computational resources to handle the deluge of genomic data, and standardized, open-source bioinformatic pipelines. Finally, we explore how technological and scientific advances will realize the promise of total biodiversity assessment in a sample—from microbes to mammals—and unlock the rich information genomics exposes, opening new possibilities for merging whole-system DNA metabarcoding with (1) abundance and biomass quantification, (2) advanced modeling, such as species occupancy models, to improve species detection, (3) population genetics, (4) phylogenetics, and (5) food web and functional gene analysis. While many challenges need to be addressed to facilitate widespread adoption of environmental genomic approaches, concurrent scientific and technological advances will usher in methods to supplement existing bioassessment tools reliant on morphological and abiotic data. This expanded toolbox will help ensure that the best tool is used for the job and enable exciting integrative techniques that capitalize on multiple tools. Collectively, these new approaches will aid in addressing the global biodiversity crisis we now face.

scholarly journals Using DNA barcodes to assess identity and diversity of Dendropsophus minutus: Failure?

Zootaxa ◽  
2008 ◽  
Vol 1691 (1) ◽  
pp. 67 ◽  
Author(s):  
M. ALEX SMITH
Keyword(s):  
Cytochrome C ◽  
Small Group ◽  
Cytochrome C Oxidase ◽  
Species Identification ◽  
Mitochondrial Gene ◽  
Dna Barcode ◽  
Gene Region ◽  
Dna Barcodes ◽  
Taxonomic Groups

The 5' end (Folmer or Barcode region) of cytochrome c oxidase 1 (CO1) has been proposed as the gene region of choice for a standardized animal DNA barcode (Hebert et al. 2003). Concerns have been raised regarding the decision to utilize this particular mitochondrial gene region as a barcode. Nevertheless, widely divergent taxonomic groups have reported success using CO1 for both species identification and discovery. The utility of CO1 for barcoding amphibians was raised early on (Vences, et al. 2005) and concerns for this group were reported widely (Waugh 2007)—although some considered that the reporting of the concerns outstripped the data that had been analyzed at that point (Smith et al. 2008). Indeed, our analysis of CO1 for a small group of Holarctic amphibians was neither more difficult to generate nor to analyze than for other groups where we have utilized the technique.

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