A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples

deWaard, Jeremy R; Ratnasingham, Sujeevan; Zakharov, Evgeny; Borisenko, Alex; Steinke, Dirk; Telfer, Angela C; Perez, Kate; Sones, Jayme E; Young, Monica R; Lévesque-Beaudin, Valérie; Sobel, Crystal N; Abrahamyan, Arusyak; Bessonov, Kyrylo; Blagoev, Gergin; deWaard, Stephanie; Ho, Chris; Ivanova, Natalia V.; Layton, Kara K S; Lu, Liuqiong; Manjunath, Ramya; McKeown, Jaclyn; Milton, Megan A.; Miskie, Renee; Monkhouse, Norm; Naik, Suresh; Nikolova, Nadya; Pentinsaari, Mikko; Prosser, Sean W. J.; Radulovici, Adriana; Steinke, Claudia; Warne, Connor P; Hebert, Paul D. N.

doi:10.1038/s41597-019-0320-2

Cited by 57 publications

(38 citation statements)

References 63 publications

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“…By using three distinct taxa important in biomonitoring studies, BAGS allowed us to promptly understand the differences in the level of congruency of their available DNA barcodes and in the quality of their respective reference libraries. Recent initiatives (e.g., deWaard et al., 2019; Hobern & Hebert, 2019; Leese et al., 2016) have been striving to increase the taxonomic coverage of universal databases, however, DNA barcodes are still missing for many species (e.g., Weigand et al., 2019) or are poorly represented (high prevalence of grade D species here observed; Figure 3), reinforcing the continuous need for the completion of reference libraries.…”

Section: Discussionmentioning

confidence: 87%

BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries

Fontes

Vieira

Ekrem

et al. 2020

Molecular Ecology Resources

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Biodiversity studies greatly benefit from molecular tools, such as DNA metabarcoding, which provides an effective identification tool in biomonitoring and conservation programmes. The accuracy of species‐level assignment, and consequent taxonomic coverage, relies on comprehensive DNA barcode reference libraries. The role of these libraries is to support species identification, but accidental errors in the generation of the barcodes may compromise their accuracy. Here, we present an R‐based application, Barcode, Audit & Grade System (BAGS) (https://github.com/tadeu95/BAGS), that performs automated auditing and annotation of cytochrome c oxidase subunit I (COI) sequences libraries, for a given taxonomic group of animals, available in the Barcode of Life Data System (BOLD). This is followed by implementing a qualitative ranking system that assigns one of five grades (A to E) to each species in the reference library, according to the attributes of the data and congruency of species names with sequences clustered in barcode index numbers (BINs). Our goal is to allow researchers to obtain the most useful and reliable data, highlighting and segregating records according to their congruency. Different tests were performed to perceive its usefulness and limitations. BAGS fulfils a significant gap in the current landscape of DNA barcoding research tools by quickly screening reference libraries to gauge the congruence status of data and facilitate the triage of ambiguous data for posterior review. Thereby, BAGS has the potential to become a valuable addition in forthcoming DNA metabarcoding studies, in the long term contributing to globally improve the quality and reliability of the public reference libraries.

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Section: Discussionmentioning

confidence: 87%

BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries

Fontes

Vieira

Ekrem

et al. 2020

Molecular Ecology Resources

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“…This study identifies existing gaps in barcode libraries for Mojave Desert biota and taxonomist ground surveys (e.g., plants and rodents), limiting the conclusions drawn from eDNA metabarcoding biodiversity assessments for environmental management of Mojave Desert spring ecosystems. Future efforts and resources will need to focus on creating reference databases for commonly used barcodes by prioritizing sequencing efforts based on species lists generated by ground surveys (e.g., camera trap images and botanical surveys) from voucher specimens (e.g., deWaard et al., 2019) and include advanced technology (e.g., artificial intelligence of camera trap data, Norouzzadeh et al., 2018; Tabak et al., 2019).…”

Section: Discussionmentioning

confidence: 99%

The utility of environmental DNA from sediment and water samples for recovery of observed plant and animal species from four Mojave Desert springs

et al. 2020

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Mojave Desert springs are fragile ecosystems, hosting endemic plants and animals, which are threatened by the increasing human demand for water and climate change. To develop management practices that will protect the groundwater‐dependent ecosystems at Mojave Desert springs, real‐time, low‐cost biodiversity monitoring, and assessments are required. Environmental DNA (eDNA) metabarcoding uses DNA shed from organisms (e.g., skin cells, feces, and pollen) that are present in water, air, soil, or sediment samples to assess community composition. This approach can increase the detection sensitivity for rare and elusive species, compared with expensive and time‐consuming conventional methods, which also require taxonomic expertise. This study tests the effectiveness of eDNA techniques in capturing the observed Mojave Desert spring biodiversity in the winter and spring of 2019 at four distinct, naturally occurring springs. We also test the utility of sample types (water vs. sediment) for capturing biodiversity. We found that each of the four Mojave Desert springs supports a unique biological community. Sediment samples contained the greatest biodiversity, but all sample types captured species observed in the field by humans or camera traps. We also found no statistical difference in species richness captured in winter and spring except for the Cytochrome Oxidase I marker, for which winter had greater biodiversity. This study supports the use of eDNA metabarcoding as an effective tool to mirror observation by human observers of ecological communities in desert springs. The study demonstrates the importance of appropriately timing eDNA field sampling, primer selection, and using field‐based surveys of wildlife and plants in addition to eDNA detection. This study also identified gaps in reference sequence databases for Mojave biodiversity and encourages collaboration of eDNA researchers with managers for effective conservation management plans.

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“…It is not known how far north the species spans along the coasts of Canada. Intriguingly, the most northern genetically studied population, from Hudson Bay (58.5 N) appeared to be predominantly M. edulis (the NCBI collection of the DNA barcode study of Canadian invertebrates [93]). Along the western coast of Greenland, M. edulis populations appear to be taken over by M. trossulus at 70.5 • N (GLL, GLD) where these two species form a hybrid zone [25].…”

Section: Distribution Of Mytilus Taxa On the Coasts Of North Atlanticmentioning

confidence: 99%

Trans-Atlantic Distribution and Introgression as Inferred from Single Nucleotide Polymorphism: Mussels Mytilus and Environmental Factors

Wenne

Zbawicka

Bach

et al. 2020

Genes

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Large-scale climate changes influence the geographic distribution of biodiversity. Many taxa have been reported to extend or reduce their geographic range, move poleward or displace other species. However, for closely related species that can hybridize in the natural environment, displacement is not the only effect of changes of environmental variables. Another option is subtler, hidden expansion, which can be found using genetic methods only. The marine blue mussels Mytilus are known to change their geographic distribution despite being sessile animals. In addition to natural dissemination at larval phase—enhanced by intentional or accidental introductions and rafting—they can spread through hybridization and introgression with local congeners, which can create mixed populations sustaining in environmental conditions that are marginal for pure taxa. The Mytilus species have a wide distribution in coastal regions of the Northern and Southern Hemisphere. In this study, we investigated the inter-regional genetic differentiation of the Mytilus species complex at 53 locations in the North Atlantic and adjacent Arctic waters and linked this genetic variability to key local environmental drivers. Of seventy-nine candidate single nucleotide polymorphisms (SNPs), all samples were successfully genotyped with a subset of 54 SNPs. There was a clear interregional separation of Mytilus species. However, all three Mytilus species hybridized in the contact area and created hybrid zones with mixed populations. Boosted regression trees (BRT) models showed that inter-regional variability was important in many allele models but did not prevail over variability in local environmental factors. Local environmental variables described over 40% of variability in about 30% of the allele frequencies of Mytilus spp. For the 30% of alleles, variability in their frequencies was only weakly coupled with local environmental conditions. For most studied alleles the linkages between environmental drivers and the genetic variability of Mytilus spp. were random in respect to “coding” and “non-coding” regions. An analysis of the subset of data involving functional genes only showed that two SNPs at Hsp70 and ATPase genes correlated with environmental variables. Total predictive ability of the highest performing models (r2 between 0.550 and 0.801) were for alleles that discriminated most effectively M. trossulus from M. edulis and M. galloprovincialis, whereas the best performing allele model (BM101A) did the best at discriminating M. galloprovincialis from M. edulis and M. trossulus. Among the local environmental variables, salinity, water temperature, ice cover and chlorophyll a concentration were by far the greatest predictors, but their predictive performance varied among different allele models. In most cases changes in the allele frequencies along these environmental gradients were abrupt and occurred at a very narrow range of environmental variables. In general, regions of change in allele frequencies for M. trossulus occurred at 8–11 psu, 0–10 °C, 60%–70% of ice cover and 0–2 mg m−3 of chlorophyll a, M. edulis at 8–11 and 30–35 psu, 10–14 °C and 60%–70% of ice cover and for M. galloprovincialis at 30–35 psu, 14–20 °C.

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A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples

Cited by 57 publications

References 63 publications

BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries

BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries

The utility of environmental DNA from sediment and water samples for recovery of observed plant and animal species from four Mojave Desert springs

Trans-Atlantic Distribution and Introgression as Inferred from Single Nucleotide Polymorphism: Mussels Mytilus and Environmental Factors

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