Publications by authors named "Jeremy R Dewaard"

37 Publications

DNA barcodes enable higher taxonomic assignments in the Acari.

Sci Rep 2021 Aug 5;11(1):15922. Epub 2021 Aug 5.

Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.

Although mites (Acari) are abundant in many terrestrial and freshwater ecosystems, their diversity is poorly understood. Since most mite species can be distinguished by variation in the DNA barcode region of cytochrome c oxidase I, the Barcode Index Number (BIN) system provides a reliable species proxy that facilitates large-scale surveys. Such analysis reveals many new BINs that can only be identified as Acari until they are examined by a taxonomic specialist. This study demonstrates that the Barcode of Life Datasystem's identification engine (BOLD ID) generally delivers correct ordinal and family assignments from both full-length DNA barcodes and their truncated versions gathered in metabarcoding studies. This result was demonstrated by examining BOLD ID's capacity to assign 7021 mite BINs to their correct order (4) and family (189). Identification success improved with sequence length and taxon coverage but varied among orders indicating the need for lineage-specific thresholds. A strict sequence similarity threshold (86.6%) prevented all ordinal misassignments and allowed the identification of 78.6% of the 7021 BINs. However, higher thresholds were required to eliminate family misassignments for Sarcoptiformes (89.9%), and Trombidiformes (91.4%), consequently reducing the proportion of BINs identified to 68.6%. Lineages with low barcode coverage in the reference library should be prioritized for barcode library expansion to improve assignment success.
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http://dx.doi.org/10.1038/s41598-021-95147-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8342613PMC
August 2021

A DNA barcode library for the butterflies of North America.

PeerJ 2021 19;9:e11157. Epub 2021 Apr 19.

Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.

Although the butterflies of North America have received considerable taxonomic attention, overlooked species and instances of hybridization continue to be revealed. The present study assembles a DNA barcode reference library for this fauna to identify groups whose patterns of sequence variation suggest the need for further taxonomic study. Based on 14,626 records from 814 species, DNA barcodes were obtained for 96% of the fauna. The maximum intraspecific distance averaged 1/4 the minimum distance to the nearest neighbor, producing a barcode gap in 76% of the species. Most species (80%) were monophyletic, the others were para- or polyphyletic. Although 15% of currently recognized species shared barcodes, the incidence of such taxa was far higher in regions exposed to Pleistocene glaciations than in those that were ice-free. Nearly 10% of species displayed high intraspecific variation (>2.5%), suggesting the need for further investigation to assess potential cryptic diversity. Aside from aiding the identification of all life stages of North American butterflies, the reference library has provided new perspectives on the incidence of both cryptic and potentially over-split species, setting the stage for future studies that can further explore the evolutionary dynamics of this group.
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http://dx.doi.org/10.7717/peerj.11157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8061581PMC
April 2021

Torix Rickettsia are widespread in arthropods and reflect a neglected symbiosis.

Gigascience 2021 Mar;10(3)

Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Leahurst Campus, Chester High Road, Neston, Wirral CH64 7TE, UK.

Background: Rickettsia are intracellular bacteria best known as the causative agents of human and animal diseases. Although these medically important Rickettsia are often transmitted via haematophagous arthropods, other Rickettsia, such as those in the Torix group, appear to reside exclusively in invertebrates and protists with no secondary vertebrate host. Importantly, little is known about the diversity or host range of Torix group Rickettsia.

Results: This study describes the serendipitous discovery of Rickettsia amplicons in the Barcode of Life Data System (BOLD), a sequence database specifically designed for the curation of mitochondrial DNA barcodes. Of 184,585 barcode sequences analysed, Rickettsia is observed in ∼0.41% of barcode submissions and is more likely to be found than Wolbachia (0.17%). The Torix group of Rickettsia are shown to account for 95% of all unintended amplifications from the genus. A further targeted PCR screen of 1,612 individuals from 169 terrestrial and aquatic invertebrate species identified mostly Torix strains and supports the "aquatic hot spot" hypothesis for Torix infection. Furthermore, the analysis of 1,341 SRA deposits indicates that Torix infections represent a significant proportion of all Rickettsia symbioses found in arthropod genome projects.

Conclusions: This study supports a previous hypothesis that suggests that Torix Rickettsia are overrepresented in aquatic insects. In addition, multiple methods reveal further putative hot spots of Torix Rickettsia infection, including in phloem-feeding bugs, parasitoid wasps, spiders, and vectors of disease. The unknown host effects and transmission strategies of these endosymbionts make these newly discovered associations important to inform future directions of investigation involving the understudied Torix Rickettsia.
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http://dx.doi.org/10.1093/gigascience/giab021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7992394PMC
March 2021

Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis.

Mol Ecol 2021 03 2;30(5):1120-1135. Epub 2021 Feb 2.

Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Spain.

High-throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site-based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the nonmicrobial terrestrial domain, an international symposium entitled "Next Generation Biodiversity Monitoring" was held in November 2019 in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarize the consensus that emerged from the 3-day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS-based strategy to collectively build an integrative framework for site-based biodiversity data generation.
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http://dx.doi.org/10.1111/mec.15797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7986105PMC
March 2021

Using DNA-barcoded Malaise trap samples to measure impact of a geothermal energy project on the biodiversity of a Costa Rican old-growth rain forest.

Genome 2020 Sep 24;63(9):407-436. Epub 2020 Jun 24.

Japan International Cooperation Agency, Tokyo, Japan.

We report one year (2013-2014) of biomonitoring an insect community in a tropical old-growth rain forest, during construction of an industrial-level geothermal electricity project. This is the first-year reaction by the species-rich insect biodiversity; six subsequent years are being analyzed now. The site is on the margin of a UNESCO Natural World Heritage Site, Área de Conservación Guanacaste (ACG), in northwestern Costa Rica. This biomonitoring is part of Costa Rica's ongoing efforts to sustainably retain its wild biodiversity through biodevelopmental integration with its societies. Essential tools are geothermal engineering needs, entomological knowledge, insect species-rich forest, government-NGO integration, common sense, DNA barcoding for species-level identification, and Malaise traps. This research is tailored for integration with its society at the product level. We combine an academic view with on-site engineering decisions. This biomonitoring requires alpha-level DNA barcoding combined with centuries of morphology-based entomological taxonomy and ecology. Not all desired insect community analyses are performed; they are for data from subsequent years combined with this year. We provide enough analysis to be used by both guilds now. This biomonitoring has shown, for the first year, that the geothermal project impacts only the biodiversity within a zone less than 50 m from the project margin.
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http://dx.doi.org/10.1139/gen-2020-0002DOI Listing
September 2020

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

Sci Data 2019 12 6;6(1):308. Epub 2019 Dec 6.

Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.

The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet's land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.
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http://dx.doi.org/10.1038/s41597-019-0320-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6897906PMC
December 2019

DNA barcodes expose unexpected diversity in Canadian mites.

Mol Ecol 2019 12 22;28(24):5347-5359. Epub 2019 Nov 22.

Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada.

Mites (Arachnida: Acariformes, Parasitiformes) are the most abundant and species-rich group of arthropods in soil, but are also diverse in freshwater habitats, on plants, and as symbionts of larger animals. However, assessment of their diversity has been impeded by their small size and often cryptic morphology. As a consequence, published estimates of their species richness span more than two orders of magnitude (0.4-114 million). In this study we employ DNA barcoding and the Barcode Index Number (BIN) system to investigate mite diversity at over 1,800 sites across Canada, primarily from soil and litter habitats with smaller contributions from freshwater, plants, and animal hosts. Barcodes from 73,394 specimens revealed 7,077 BINs with representatives from all four orders (Ixodida, Mesostigmata, Sarcoptiformes, Trombidiformes) and 60% (186) of the known families. The BIN total is 2.4 times the number of species previously recorded from Canada (2,999), reflecting the unexpectedly high richness of several families. Richness projections suggest that more than 28,000 BINs occur at the sampled locations, indicating that the Canadian mite fauna almost certainly includes more than 30,000 species-a total similar to that for the most diverse insect order in Canada, Diptera. This unexpected diversity was partitioned into highly dissimilar, spatially-structured assemblages that likely reflect dispersal limitation and environmental heterogeneity. Further sampling of a greater diversity of habitats will refine understanding of mite diversity in Canada, but similar analyses in other geographic regions will be essential to ascertain their diversity at a global scale.
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http://dx.doi.org/10.1111/mec.15292DOI Listing
December 2019

Trichoptera of Canada.

Zookeys 2019 24(819):507-520. Epub 2019 Jan 24.

Center for Water Resources, College of Agriculture and Food Sciences, Florida A&M University, 113 South Perry-Paige Bldg., Tallahassee, Florida 32307-4100, USA Florida A&M University Tallahassee United States of America.

Trichoptera, or caddisflies, are common members of freshwater ecosystems as larvae and are important indicators of aquatic system health. As such, the species are relatively well studied, with keys available for larvae and adults of many of the taxa occurring in Canada. The number of species recorded from Canada since 1979 (Wiggins 1979) has increased from 546 to 636, an increase of 16.4%. Of those species newly recorded, 17 represent newly described taxa since 1979. Taking into consideration the species likely to be subsequently found in Canada based on records in adjacent parts of the United States and results from DNA barcoding, an estimated 129-181 species remain to be documented in Canada.
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http://dx.doi.org/10.3897/zookeys.819.31140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355732PMC
January 2019

Lepidoptera of Canada.

Zookeys 2019 24(819):463-505. Epub 2019 Jan 24.

Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada University of Guelph Guelph Canada.

The known Lepidoptera (moths and butterflies) of the provinces and territories of Canada are summarised, and current knowledge is compared to the state of knowledge in 1979. A total of 5405 species are known to occur in Canada in 81 families, and a further 50 species have been reported but are unconfirmed. This represents an increase of 1348 species since 1979. The DNA barcodes available for Canadian Lepidoptera are also tabulated, based on a dataset of 148,314 specimens corresponding to 5842 distinct clusters. A further yet-undiscovered 1400 species of Lepidoptera are estimated to occur in Canada. The Gelechioidea are the most poorly known major lineage of Lepidoptera in Canada. Nunavut, Prince Edward Island, and British Columbia are thought to show the greatest deficit in our knowledge of Lepidoptera. The unglaciated portions of the Yukon (Beringia), and the Pacific Maritime, Montane Cordillera, and Western Interior Basin ecozones of British Columbia are also identified as hotbeds of undescribed biodiversity.
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http://dx.doi.org/10.3897/zookeys.819.27259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355748PMC
January 2019

Diptera of Canada.

Zookeys 2019 24(819):397-450. Epub 2019 Jan 24.

Agriculture and Agri-Food Canada, Canadian National Collection of Insects, Arachnids and Nematodes, Ottawa, Ontario, Canada Royal British Columbia Museum Salmon Arm Canada.

The Canadian Diptera fauna is updated. Numbers of species currently known from Canada, total Barcode Index Numbers (BINs), and estimated numbers of undescribed or unrecorded species are provided for each family. An overview of recent changes in the systematics and Canadian faunistics of major groups is provided as well as some general information on biology and life history. A total of 116 families and 9620 described species of Canadian Diptera are reported, representing more than a 36% increase in species numbers since the last comparable assessment by JF McAlpine et al. (1979). Almost 30,000 BINs have so far been obtained from flies in Canada. Estimates of additional number of species remaining to be documented in the country range from 5200 to 20,400.
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http://dx.doi.org/10.3897/zookeys.819.27625DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355757PMC
January 2019

Hymenoptera of Canada.

Zookeys 2019 24(819):311-360. Epub 2019 Jan 24.

Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada University of Guelph Guelph Canada.

A summary of the numbers of species of the 83 families of Hymenoptera recorded in Canada is provided. In total, 8757 described species are recorded compared to approximately 6000 in 1979, which is a 46% increase. Of the families recognized in 1979, three have been newly recorded to Canada since the previous survey: Anaxyelidae (Anaxyleoidea), Liopteridae (Cynipoidea), and Mymarommatidae (Mymarommatoidea). More than 18,400 BINs of Canadian Hymenoptera are available in the Barcode of Life Data Systems (Ratnasingham and Hebert 2007) implying that nearly 9650 undescribed or unrecorded species of Hymenoptera may be present in Canada (and more than 10,300 when taking into account additional species that have not been DNA barcoded). The estimated number of unrecorded species is very similar to that of 1979 (10,637 species), but the percentage of the fauna described/recorded has increased from 36% in 1979 to approximately 45% in 2018. Summaries of the state of knowledge of the major groups of Hymenoptera are presented, including brief comments on numbers of species, biology, changes in classification since 1979, and relevant taxonomic references.
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http://dx.doi.org/10.3897/zookeys.819.28510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355736PMC
January 2019

Myriapoda of Canada.

Zookeys 2019 24(819):169-186. Epub 2019 Jan 24.

Department of Biological and Environmental Sciences, Georgia College and State University, 320 N. Wayne St., Milledgeville, Georgia, 31061, USA Georgia College and State University Milledgeville United States of America.

The currently documented fauna of described species of myriapods in Canada includes 54 Chilopoda, 66 Diplopoda, 23 Pauropoda, and two Symphyla, representing increases of 24, 23, 23, and one species, respectively, since 1979. Of the 145 myriapod species currently documented, 40 species are not native to Canada. The myriapods have not been well documented with DNA barcodes and no barcodes are available for Pauropoda. It is conservatively estimated that at least 93 additional myriapods species will be discovered in Canada: Chilopoda (40), Diplopoda (29), Pauropoda (17), and Symphyla (seven). In general, there is a serious dearth of knowledge about myriapods in Canada, and systematics research and surveys continue to be needed to help document the diversity and distribution of these groups in the country.
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http://dx.doi.org/10.3897/zookeys.819.29447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355731PMC
January 2019

Characterization and comparison of poorly known moth communities through DNA barcoding in two Afrotropical environments in Gabon .

Genome 2019 Mar 2;62(3):96-107. Epub 2018 Oct 2.

o Centre d'Ecologie Fonctionnelle et Evolutive (CEFE UMR 5175, CNRS-Université de Montpellier-Université Paul-Valéry Montpellier-EPHE), 1919 Route de Mende, F-34293 Montpellier, France.

Biodiversity research in tropical ecosystems-popularized as the most biodiverse habitats on Earth-often neglects invertebrates, yet invertebrates represent the bulk of local species richness. Insect communities in particular remain strongly impeded by both Linnaean and Wallacean shortfalls, and identifying species often remains a formidable challenge inhibiting the use of these organisms as indicators for ecological and conservation studies. Here we use DNA barcoding as an alternative to the traditional taxonomic approach for characterizing and comparing the diversity of moth communities in two different ecosystems in Gabon. Though sampling remains very incomplete, as evidenced by the high proportion (59%) of species represented by singletons, our results reveal an outstanding diversity. With about 3500 specimens sequenced and representing 1385 BINs (Barcode Index Numbers, used as a proxy to species) in 23 families, the diversity of moths in the two sites sampled is higher than the current number of species listed for the entire country, highlighting the huge gap in biodiversity knowledge for this country. Both seasonal and spatial turnovers are strikingly high (18.3% of BINs shared between seasons, and 13.3% between sites) and draw attention to the need to account for these when running regional surveys. Our results also highlight the richness and singularity of savannah environments and emphasize the status of Central African ecosystems as hotspots of biodiversity.
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http://dx.doi.org/10.1139/gen-2018-0063DOI Listing
March 2019

Expedited assessment of terrestrial arthropod diversity by coupling Malaise traps with DNA barcoding .

Genome 2019 Mar 26;62(3):85-95. Epub 2018 Sep 26.

a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada.

Monitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological approaches. The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly decline as high-throughput sequencing technologies advance. Aside from detailing protocols from specimen sorting to data release, this paper describes their use in a survey of arthropod diversity in a national park that examined 21 194 specimens representing 2255 species. These protocols can support arthropod monitoring programs at regional, national, and continental scales.
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http://dx.doi.org/10.1139/gen-2018-0093DOI Listing
March 2019

DNA barcodes reveal deeply neglected diversity and numerous invasions of micromoths in Madagascar .

Genome 2019 Mar 5;62(3):108-121. Epub 2018 Sep 5.

h Department of Life Sciences, Natural History Museum, Cromwell Road, SW7 5BD, United Kingdom.

Madagascar is a prime evolutionary hotspot globally, but its unique biodiversity is under threat, essentially from anthropogenic disturbance. There is a race against time to describe and protect the Madagascan endangered biota. Here we present a first molecular characterization of the micromoth fauna of Madagascar. We collected 1572 micromoths mainly using light traps in both natural and anthropogenically disturbed habitats in 24 localities across eastern and northwest Madagascar. We also collected 1384 specimens using a Malaise trap in a primary rain forest at Andasibe, eastern Madagascar. In total, we DNA barcoded 2956 specimens belonging to 1537 Barcode Index Numbers (BINs), 88.4% of which are new to BOLD. Only 1.7% of new BINs were assigned to species. Of 47 different families found, Dryadaulidae, Bucculatricidae, Bedelliidae, Batrachedridae, and Blastobasidae are newly reported for Madagascar and the recently recognized Tonzidae is confirmed. For test faunas of Canada and Australia, 98.9%-99.4% of Macroheterocera BINs exhibited the molecular synapomorphy of a phenylalanine in the 177th complete DNA barcode codon. Non-macroheteroceran BINs could thus be sifted out efficiently in the Malaise sample. The Madagascar micromoth fauna shows highest affinity with the Afrotropics (146 BINs also occur in the African continent). We found 22 recognised pests or invasive species, mostly occurring in disturbed habitats. Malaise trap samples show high temporal turnover and alpha diversity with as many as 507 BINs collected; of these, astonishingly, 499 (98.4%) were novel to BOLD and 292 (57.6%) were singletons. Our results provide a baseline for future surveys across the island.
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http://dx.doi.org/10.1139/gen-2018-0065DOI Listing
March 2019

A Sequel to Sanger: amplicon sequencing that scales.

BMC Genomics 2018 Mar 27;19(1):219. Epub 2018 Mar 27.

Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada.

Background: Although high-throughput sequencers (HTS) have largely displaced their Sanger counterparts, the short read lengths and high error rates of most platforms constrain their utility for amplicon sequencing. The present study tests the capacity of single molecule, real-time (SMRT) sequencing implemented on the SEQUEL platform to overcome these limitations, employing 658 bp amplicons of the mitochondrial cytochrome c oxidase I gene as a model system.

Results: By examining templates from more than 5000 species and 20,000 specimens, the performance of SMRT sequencing was tested with amplicons showing wide variation in GC composition and varied sequence attributes. SMRT and Sanger sequences were very similar, but SMRT sequencing provided more complete coverage, especially for amplicons with homopolymer tracts. Because it can characterize amplicon pools from 10,000 DNA extracts in a single run, the SEQUEL can reduce greatly reduce sequencing costs in comparison to first (Sanger) and second generation platforms (Illumina, Ion).

Conclusions: SMRT analysis generates high-fidelity sequences from amplicons with varying GC content and is resilient to homopolymer tracts. Analytical costs are low, substantially less than those for first or second generation sequencers. When implemented on the SEQUEL platform, SMRT analysis enables massive amplicon characterization because each instrument can recover sequences from more than 5 million DNA extracts a year.
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http://dx.doi.org/10.1186/s12864-018-4611-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870082PMC
March 2018

Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada.

Appl Plant Sci 2017 Dec 22;5(12). Epub 2017 Dec 22.

Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.

Premise Of The Study: Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada.

Methods: Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%). For 98% of the specimens, at least one of the DNA barcode regions was recovered from the plastid loci and and from the nuclear ITS2 region. We used beta regression to quantify the effects of age, type of preservation, and taxonomic affiliation (family) on DNA sequence recovery.

Results: Specimen age and method of preservation had significant effects on sequence recovery for all markers, but influenced some families more (e.g., Boraginaceae) than others (e.g., Asteraceae).

Discussion: Our DNA barcode library represents an unparalleled resource for metagenomic and ecological genetic research working on temperate and arctic biomes. An observed decline in sequence recovery with specimen age may be associated with poor primer matches, intragenomic variation (for ITS2), or inhibitory secondary compounds in some taxa.
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http://dx.doi.org/10.3732/apps.1700079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749818PMC
December 2017

Probing planetary biodiversity with DNA barcodes: The Noctuoidea of North America.

PLoS One 2017 1;12(6):e0178548. Epub 2017 Jun 1.

Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada.

This study reports the assembly of a DNA barcode reference library for species in the lepidopteran superfamily Noctuoidea from Canada and the USA. Based on the analysis of 69,378 specimens, the library provides coverage for 97.3% of the noctuoid fauna (3565 of 3664 species). In addition to verifying the strong performance of DNA barcodes in the discrimination of these species, the results indicate close congruence between the number of species analyzed (3565) and the number of sequence clusters (3816) recognized by the Barcode Index Number (BIN) system. Distributional patterns across 12 North American ecoregions are examined for the 3251 species that have GPS data while BIN analysis is used to quantify overlap between the noctuoid faunas of North America and other zoogeographic regions. This analysis reveals that 90% of North American noctuoids are endemic and that just 7.5% and 1.8% of BINs are shared with the Neotropics and with the Palearctic, respectively. One third (29) of the latter species are recent introductions and, as expected, they possess low intraspecific divergences.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178548PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453547PMC
September 2017

Calibrating the taxonomy of a megadiverse insect family: 3000 DNA barcodes from geometrid type specimens (Lepidoptera, Geometridae).

Genome 2016 Sep 22;59(9):671-84. Epub 2016 Apr 22.

d Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada.

It is essential that any DNA barcode reference library be based upon correctly identified specimens. The Barcode of Life Data Systems (BOLD) requires information such as images, geo-referencing, and details on the museum holding the voucher specimen for each barcode record to aid recognition of potential misidentifications. Nevertheless, there are misidentifications and incomplete identifications (e.g., to a genus or family) on BOLD, mainly for species from tropical regions. Unfortunately, experts are often unavailable to correct taxonomic assignments due to time constraints and the lack of specialists for many groups and regions. However, considerable progress could be made if barcode records were available for all type specimens. As a result of recent improvements in analytical protocols, it is now possible to recover barcode sequences from museum specimens that date to the start of taxonomic work in the 18th century. The present study discusses success in the recovery of DNA barcode sequences from 2805 type specimens of geometrid moths which represent 1965 species, corresponding to about 9% of the 23 000 described species in this family worldwide and including 1875 taxa represented by name-bearing types. Sequencing success was high (73% of specimens), even for specimens that were more than a century old. Several case studies are discussed to show the efficiency, reliability, and sustainability of this approach.
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http://dx.doi.org/10.1139/gen-2015-0197DOI Listing
September 2016

Counting animal species with DNA barcodes: Canadian insects.

Philos Trans R Soc Lond B Biol Sci 2016 09;371(1702)

Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1.

Recent estimates suggest that the global insect fauna includes fewer than six million species, but this projection is very uncertain because taxonomic work has been limited on some highly diverse groups. Validation of current estimates minimally requires the investigation of all lineages that are diverse enough to have a substantial impact on the final species count. This study represents a first step in this direction; it employs DNA barcoding to evaluate patterns of species richness in 27 orders of Canadian insects. The analysis of over one million specimens revealed species counts congruent with earlier results for most orders. However, Diptera and Hymenoptera were unexpectedly diverse, representing two-thirds of the 46 937 barcode index numbers (=species) detected. Correspondence checks between known species and barcoded taxa showed that sampling was incomplete, a result confirmed by extrapolations from the barcode results which suggest the occurrence of at least 94 000 species of insects in Canada, a near doubling from the prior estimate of 54 000 species. One dipteran family, the Cecidomyiidae, was extraordinarily diverse with an estimated 16 000 species, a 10-fold increase from its predicted diversity. If Canada possesses about 1% of the global fauna, as it does for known taxa, the results of this study suggest the presence of 10 million insect species with about 1.8 million of these taxa in the Cecidomyiidae. If so, the global species count for this fly family may exceed the combined total for all 142 beetle families. If extended to more geographical regions and to all hyperdiverse groups, DNA barcoding can rapidly resolve the current uncertainty surrounding a species count for the animal kingdom. A newly detailed understanding of species diversity may illuminate processes important in speciation, as suggested by the discovery that the most diverse insect lineages in Canada employ an unusual mode of reproduction, haplodiploidy.This article is part of the themed issue 'From DNA barcodes to biomes'.
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http://dx.doi.org/10.1098/rstb.2015.0333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971185PMC
September 2016

DNA barcodes from century-old type specimens using next-generation sequencing.

Mol Ecol Resour 2016 03 26;16(2):487-97. Epub 2015 Oct 26.

Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada.

Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are often more than a century old and have experienced conditions unfavourable for DNA preservation, success in sequence recovery has been uncertain. This study addresses this challenge by employing next-generation sequencing (NGS) to recover sequences for the barcode region of the cytochrome c oxidase 1 gene from small amounts of template DNA. DNA quality was first screened in more than 1800 century-old type specimens of Lepidoptera by attempting to recover 164-bp and 94-bp reads via Sanger sequencing. This analysis permitted the assignment of each specimen to one of three DNA quality categories--high (164-bp sequence), medium (94-bp sequence) or low (no sequence). Ten specimens from each category were subsequently analysed via a PCR-based NGS protocol requiring very little template DNA. It recovered sequence information from all specimens with average read lengths ranging from 458 bp to 610 bp for the three DNA categories. By sequencing ten specimens in each NGS run, costs were similar to Sanger analysis. Future increases in the number of specimens processed in each run promise substantial reductions in cost, making it possible to anticipate a future where barcode sequences are available from most type specimens.
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http://dx.doi.org/10.1111/1755-0998.12474DOI Listing
March 2016

Biodiversity inventories in high gear: DNA barcoding facilitates a rapid biotic survey of a temperate nature reserve.

Biodivers Data J 2015 30(3):e6313. Epub 2015 Aug 30.

Biodiversity Institute of Ontario, Guelph, Canada.

Background: Comprehensive biotic surveys, or 'all taxon biodiversity inventories' (ATBI), have traditionally been limited in scale or scope due to the complications surrounding specimen sorting and species identification. To circumvent these issues, several ATBI projects have successfully integrated DNA barcoding into their identification procedures and witnessed acceleration in their surveys and subsequent increase in project scope and scale. The Biodiversity Institute of Ontario partnered with the rare Charitable Research Reserve and delegates of the 6th International Barcode of Life Conference to complete its own rapid, barcode-assisted ATBI of an established land trust in Cambridge, Ontario, Canada.

New Information: The existing species inventory for the rare Charitable Research Reserve was rapidly expanded by integrating a DNA barcoding workflow with two surveying strategies - a comprehensive sampling scheme over four months, followed by a one-day bioblitz involving international taxonomic experts. The two surveys resulted in 25,287 and 3,502 specimens barcoded, respectively, as well as 127 human observations. This barcoded material, all vouchered at the Biodiversity Institute of Ontario collection, covers 14 phyla, 29 classes, 117 orders, and 531 families of animals, plants, fungi, and lichens. Overall, the ATBI documented 1,102 new species records for the nature reserve, expanding the existing long-term inventory by 49%. In addition, 2,793 distinct Barcode Index Numbers (BINs) were assigned to genus or higher level taxonomy, and represent additional species that will be added once their taxonomy is resolved. For the 3,502 specimens, the collection, sequence analysis, taxonomic assignment, data release and manuscript submission by 100+ co-authors all occurred in less than one week. This demonstrates the speed at which barcode-assisted inventories can be completed and the utility that barcoding provides in minimizing and guiding valuable taxonomic specialist time. The final product is more than a comprehensive biotic inventory - it is also a rich dataset of fine-scale occurrence and sequence data, all archived and cross-linked in the major biodiversity data repositories. This model of rapid generation and dissemination of essential biodiversity data could be followed to conduct regional assessments of biodiversity status and change, and potentially be employed for evaluating progress towards the Aichi Targets of the Strategic Plan for Biodiversity 2011-2020.
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http://dx.doi.org/10.3897/BDJ.3.e6313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568406PMC
September 2015

Untangling taxonomy: a DNA barcode reference library for Canadian spiders.

Mol Ecol Resour 2016 01 26;16(1):325-41. Epub 2015 Jul 26.

Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada.

Approximately 1460 species of spiders have been reported from Canada, 3% of the global fauna. This study provides a DNA barcode reference library for 1018 of these species based upon the analysis of more than 30,000 specimens. The sequence results show a clear barcode gap in most cases with a mean intraspecific divergence of 0.78% vs. a minimum nearest-neighbour (NN) distance averaging 7.85%. The sequences were assigned to 1359 Barcode index numbers (BINs) with 1344 of these BINs composed of specimens belonging to a single currently recognized species. There was a perfect correspondence between BIN membership and a known species in 795 cases, while another 197 species were assigned to two or more BINs (556 in total). A few other species (26) were involved in BIN merges or in a combination of merges and splits. There was only a weak relationship between the number of specimens analysed for a species and its BIN count. However, three species were clear outliers with their specimens being placed in 11-22 BINs. Although all BIN splits need further study to clarify the taxonomic status of the entities involved, DNA barcodes discriminated 98% of the 1018 species. The present survey conservatively revealed 16 species new to science, 52 species new to Canada and major range extensions for 426 species. However, if most BIN splits detected in this study reflect cryptic taxa, the true species count for Canadian spiders could be 30-50% higher than currently recognized.
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http://dx.doi.org/10.1111/1755-0998.12444DOI Listing
January 2016

Streamlining the use of BOLD specimen data to record species distributions: a case study with ten Nearctic species of Microgastrinae (Hymenoptera: Braconidae).

Biodivers Data J 2014 29(2):e4153. Epub 2014 Oct 29.

Biodiversity Institute of Ontario, University of Guelph, Guelph, Canada.

The Barcode of Life Data Systems (BOLD) is designed to support the generation and application of DNA barcode data, but it also provides a unique source of data with potential for many research uses. This paper explores the streamlining of BOLD specimen data to record species distributions - and its fast publication using the Biodiversity Data Journal (BDJ), and its authoring platform, the Pensoft Writing Tool (PWT). We selected a sample of 630 specimens and 10 species of a highly diverse group of parasitoid wasps (Hymenoptera: Braconidae, Microgastrinae) from the Nearctic region and used the information in BOLD to uncover a significant number of new records (of locality, provinces, territories and states). By converting specimen information (such as locality, collection date, collector, voucher depository) from the BOLD platform to the Excel template provided by the PWT, it is possible to quickly upload and generate long lists of "Material Examined" for papers discussing taxonomy, ecology and/or new distribution records of species. For the vast majority of publications including DNA barcodes, the generation and publication of ancillary data associated with the barcoded material is seldom highlighted and often disregarded, and the analysis of those data sets to uncover new distribution patterns of species has rarely been explored, even though many BOLD records represent new and/or significant discoveries. The introduction of journals specializing in - and streamlining - the release of these datasets, such as the BDJ, should facilitate thorough analysis of these records, as shown in this paper.
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http://dx.doi.org/10.3897/BDJ.2.e4153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4251541PMC
December 2014

A transcontinental challenge--a test of DNA barcode performance for 1,541 species of Canadian Noctuoidea (Lepidoptera).

PLoS One 2014 25;9(3):e92797. Epub 2014 Mar 25.

Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada.

This study provides a first, comprehensive, diagnostic use of DNA barcodes for the Canadian fauna of noctuoids or "owlet" moths (Lepidoptera: Noctuoidea) based on vouchered records for 1,541 species (99.1% species coverage), and more than 30,000 sequences. When viewed from a Canada-wide perspective, DNA barcodes unambiguously discriminate 90% of the noctuoid species recognized through prior taxonomic study, and resolution reaches 95.6% when considered at a provincial scale. Barcode sharing is concentrated in certain lineages with 54% of the cases involving 1.8% of the genera. Deep intraspecific divergence exists in 7.7% of the species, but further studies are required to clarify whether these cases reflect an overlooked species complex or phylogeographic variation in a single species. Non-native species possess higher Nearest-Neighbour (NN) distances than native taxa, whereas generalist feeders have lower NN distances than those with more specialized feeding habits. We found high concordance between taxonomic names and sequence clusters delineated by the Barcode Index Number (BIN) system with 1,082 species (70%) assigned to a unique BIN. The cases of discordance involve both BIN mergers and BIN splits with 38 species falling into both categories, most likely reflecting bidirectional introgression. One fifth of the species are involved in a BIN merger reflecting the presence of 158 species sharing their barcode sequence with at least one other taxon, and 189 species with low, but diagnostic COI divergence. A very few cases (13) involved species whose members fell into both categories. Most of the remaining 140 species show a split into two or three BINs per species, while Virbia ferruginosa was divided into 16. The overall results confirm that DNA barcodes are effective for the identification of Canadian noctuoids. This study also affirms that BINs are a strong proxy for species, providing a pathway for a rapid, accurate estimation of animal diversity.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0092797PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965468PMC
December 2014

A DNA 'barcode blitz': rapid digitization and sequencing of a natural history collection.

PLoS One 2013 10;8(7):e68535. Epub 2013 Jul 10.

Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada.

DNA barcoding protocols require the linkage of each sequence record to a voucher specimen that has, whenever possible, been authoritatively identified. Natural history collections would seem an ideal resource for barcode library construction, but they have never seen large-scale analysis because of concerns linked to DNA degradation. The present study examines the strength of this barrier, carrying out a comprehensive analysis of moth and butterfly (Lepidoptera) species in the Australian National Insect Collection. Protocols were developed that enabled tissue samples, specimen data, and images to be assembled rapidly. Using these methods, a five-person team processed 41,650 specimens representing 12,699 species in 14 weeks. Subsequent molecular analysis took about six months, reflecting the need for multiple rounds of PCR as sequence recovery was impacted by age, body size, and collection protocols. Despite these variables and the fact that specimens averaged 30.4 years old, barcode records were obtained from 86% of the species. In fact, one or more barcode compliant sequences (>487 bp) were recovered from virtually all species represented by five or more individuals, even when the youngest was 50 years old. By assembling specimen images, distributional data, and DNA barcode sequences on a web-accessible informatics platform, this study has greatly advanced accessibility to information on thousands of species. Moreover, much of the specimen data became publically accessible within days of its acquisition, while most sequence results saw release within three months. As such, this study reveals the speed with which DNA barcode workflows can mobilize biodiversity data, often providing the first web-accessible information for a species. These results further suggest that existing collections can enable the rapid development of a comprehensive DNA barcode library for the most diverse compartment of terrestrial biodiversity - insects.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068535PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707885PMC
March 2014

Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology.

Zootaxa 2013 Dec 16;3749:1-93. Epub 2013 Dec 16.

Biodiversity Institute of Ontario, University of Guelph, Guelph ON N1G 2W1 Canada.; Email:

This study reports 30 species of Lepidoptera previously known from either the Palearctic or the Nearctic that are newly recorded as Holarctic. For 28 of these species, their intercontinental distributions were initially detected through DNA barcode analysis and subsequently confirmed by morphological examination; two Palearctic species were first detected in North America through morphology and then barcoded. When possible, the origin and status of each species (introduced, overlooked Holarctic species, or unknowingly re-described) is discussed, and its morphology is diagnosed and illustrated. The species involved include Tineidae: Scardia amurensis Zagulajev, Triaxomera parasitella (Hübner), Nemapogon cloacella (Haworth), Elatobia montelliella (Schantz), Tinea svenssoni Opheim; Gracillariidae: Caloptilia suberinella (Tengström), Parornix betulae (Stainton); Phyllonorycter maestingella (Müller); Yponomeutidae: Paraswammerdamia albicapitella (Scharfenberg), P. conspersella (Tengström); Plutellidae: Plutella hyperboreella Strand; Lyonetiidae: Lyonetia pulverulentella Zeller; Autostichidae: Oegoconia deauratella (Herrich-Schäffer), O. novimundi (Busck); Blastobasidae: Blastobasis glandulella (Riley), B. maroccanella (Amsel), B. tarda Meyrick; Depressariidae: Agonopterix conterminella (Zeller), Depressaria depressana (F.); Coleophoridae: Coleophora atriplicis Meyrick, C. glitzella Hofmann, C. granulatella Zeller, C. texanella Chambers, C. vitisella Gregson; Scythrididae: Scythris sinensis (Felder & Rogenhofer); Gelechiidae: Altenia perspersella (Wocke), Gnorimoschema jalavai Povolný, Scrobipalpa acuminatella (Sircom), Sophronia gelidella Nordman; Choreutidae: Anthophila fabriciana (L.); and Tortricidae: Phiaris bipunctana (F.). These cases of previously unrecognized faunal overlap have led to their redescription in several instances. Five new synonyms are proposed: Blastobasis glandulella (Riley, 1871) = B. huemeri Sinev, 1993, syn. nov.; B. tarda Meyrick, 1902 = Neoblastobasis ligurica Nel & Varenne, 2004, syn. nov.; Coleophora atriplicis Meyrick, 1928 = C. cervinella McDunnough, 1946, syn. nov.; C. texanella Chambers, 1878 = C. coxi Baldizzone & van der Wolf, 2007, syn. nov., and = C. vagans Walsingham, 1907, syn. nov. Lectotypes are designated for Blastobasis tarda Meyrick and Coleophora texanella Chambers. Type specimens were examined where pertinent to establish new synonymies. We identify 12 previously overlooked cases of species introductions, highlighting the power of DNA barcoding as a tool for biosurveillance.
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http://dx.doi.org/10.11646/zootaxa.3749.1.1DOI Listing
December 2013

A comprehensive DNA barcode library for the looper moths (Lepidoptera: Geometridae) of British Columbia, Canada.

PLoS One 2011 Mar 28;6(3):e18290. Epub 2011 Mar 28.

Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada.

Background: The construction of comprehensive reference libraries is essential to foster the development of DNA barcoding as a tool for monitoring biodiversity and detecting invasive species. The looper moths of British Columbia (BC), Canada present a challenging case for species discrimination via DNA barcoding due to their considerable diversity and limited taxonomic maturity.

Methodology/principal Findings: By analyzing specimens held in national and regional natural history collections, we assemble barcode records from representatives of 400 species from BC and surrounding provinces, territories and states. Sequence variation in the barcode region unambiguously discriminates over 93% of these 400 geometrid species. However, a final estimate of resolution success awaits detailed taxonomic analysis of 48 species where patterns of barcode variation suggest cases of cryptic species, unrecognized synonymy as well as young species.

Conclusions/significance: A catalog of these taxa meriting further taxonomic investigation is presented as well as the supplemental information needed to facilitate these investigations.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018290PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065486PMC
March 2011

Towards a global barcode library for Lymantria (Lepidoptera: Lymantriinae) tussock moths of biosecurity concern.

PLoS One 2010 Dec 9;5(12):e14280. Epub 2010 Dec 9.

Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada.

Background: Detecting and controlling the movements of invasive species, such as insect pests, relies upon rapid and accurate species identification in order to initiate containment procedures by the appropriate authorities. Many species in the tussock moth genus Lymantria are significant forestry pests, including the gypsy moth Lymantria dispar L., and consequently have been a focus for the development of molecular diagnostic tools to assist in identifying species and source populations. In this study we expand the taxonomic and geographic coverage of the DNA barcode reference library, and further test the utility of this diagnostic method, both for species/subspecies assignment and for determination of geographic provenance of populations.

Methodology/principal Findings: Cytochrome oxidase I (COI) barcodes were obtained from 518 individuals and 36 species of Lymantria, including sequences assembled and generated from previous studies, vouchered material in public collections, and intercepted specimens obtained from surveillance programs in Canada. A maximum likelihood tree was constructed, revealing high bootstrap support for 90% of species clusters. Bayesian species assignment was also tested, and resulted in correct assignment to species and subspecies in all instances. The performance of barcoding was also compared against the commonly employed NB restriction digest system (also based on COI); while the latter is informative for discriminating gypsy moth subspecies, COI barcode sequences provide greater resolution and generality by encompassing a greater number of haplotypes across all Lymantria species, none shared between species.

Conclusions/significance: This study demonstrates the efficacy of DNA barcodes for diagnosing species of Lymantria and reinforces the view that the approach is an under-utilized resource with substantial potential for biosecurity and surveillance. Biomonitoring agencies currently employing the NB restriction digest system would gather more information by transitioning to the use of DNA barcoding, a change which could be made relatively seamlessly as the same gene region underlies both protocols.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0014280PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000334PMC
December 2010
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