Testing use of mitochondrial COI sequences for the identification and phylogenetic analysis of New Zealand caddisflies (Trichoptera)

We tested the hypothesis that cytochrome c oxidase subunit 1 (COI) sequences would successfully discriminate recognised species of New Zealand caddisflies. We further examined whether phylogenetic analyses, based on the COI locus, could recover currently recognised superfamilies and suborders. COI sequences were obtained from 105 individuals representing 61 species and all 16 families of Trichoptera known from New Zealand. No sequence sharing was observed between members of different species, and congeneric species showed from 2.3 to 19.5% divergence. Sequence divergence among members of a species was typically low (mean = 0.7%; range 0.0–8.5%), but two species showed intraspecific divergences in excess of 2%. Phylogenetic reconstructions based on COI were largely congruent with previous conclusions based on morphology, although the sequence data did not support placement of the purse-cased caddisflies (Hydroptilidae) within the uncased caddisflies, and, in particular, the Rhyacophiloidea. We conclude that sequence variation in the COI gene locus is an effective tool for the identification of New Zealand caddisfly species, and can provide preliminary phylogenetic inferences. Further research is needed to ascertain the significance of the few instances of high intra-specific divergence and to determine if any instances of sequence sharing will be detected with larger sample sizes

DNA barcodes for 1/1000 of the animal kingdom

This study reports DNA barcodes for more than 1300 Lepidoptera species from the eastern half of North America, establishing that 99.3 per cent of these species possess diagnostic barcode sequences. Intraspecific divergences averaged just 0.43 per cent among this assemblage, but most values were lower. The mean was elevated by deep barcode divergences (greater than 2%) in 5.1 per cent of the species, often involving the sympatric occurrence of two barcode clusters. A few of these cases have been analysed in detail, revealing species overlooked by the current taxonomic system. This study also provided a large-scale test of the extent of regional divergence in barcode sequences, indicating that geographical differentiation in the Lepidoptera of eastern North America is small, even when comparisons involve populations as much as 2800 km apart. The present results affirm that a highly effective system for the identification of Lepidoptera in this region can be built with few records per species because of the limited intra-specific variation. As most terrestrial and marine taxa are likely to possess a similar pattern of population structure, an effective DNA-based identification system can be developed with modest effort

Myriapoda of Canada

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

In the dark in a large urban park: DNA barcodes illuminate cryptic and introduced moth species

Abstract To facilitate future assessments of diversity following disturbance events, we conducted a first level inventory of nocturnal Lepidoptera in Stanley Park, Vancouver, Canada. To aid the considerable task, we employed high-throughput DNA barcoding for the rough sorting of all material and for tentative species identifications, where possible. We report the preliminary species list of 190, the detection of four new exotic species (Argyresthia pruniella, Dichelia histrionana, Paraswammerdamia lutarea, and Prays fraxinella), and the potential discovery of two cryptic species. We describe the magnitude of assistance that barcoding presents for faunal inventories, from reducing specialist time to facilitating the detection of native and exotic species at low density

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

The synthesis of this dataset was enabled by funding from the Canada Foundation for Innovation, from Genome Canada through Ontario Genomics, from NSERC, and from the Ontario Ministry of Research, Innovation and Science in support of the International Barcode of Life project. It was also enabled by philanthropic support from the Gordon and Betty Moore Foundation and from Ann McCain Evans and Chris Evans. The release of the data on GGBN was supported by a GGBN – Global Genome Initiative Award and we thank G. Droege, L. Loo, K. Barker, and J. Coddington for their support. Our work depended heavily on the analytical capabilities of the Barcode of Life Data Systems (BOLD, www.boldsystems.org). We also thank colleagues at the CBG for their support, including S. Adamowicz, S. Bateson, E. Berzitis, V. Breton, V. Campbell, A. Castillo, C. Christopoulos, J. Cossey, C. Gallant, J. Gleason, R. Gwiazdowski, M. Hajibabaei, R. Hanner, K. Hough, P. Janetta, A. Pawlowski, S. Pedersen, J. Robertson, D. Roes, K. Seidle, M. A. Smith, B. St. Jacques, A. Stoneham, J. Stahlhut, R. Tabone, J.Topan, S. Walker, and C. Wei. For bioblitz-related assistance, we are grateful to D. Ireland, D. Metsger, A. Guidotti, J. Quinn and other members of Bioblitz Canada and Ontario Bioblitz. For our work in Canada’s national parks, we thank S. Woodley and J. Waithaka for their lead role in organizing permits and for the many Parks Canada staff who facilitated specimen collections, including M. Allen, D. Amirault-Langlais, J. Bastick, C. Belanger, C. Bergman, J.-F. Bisaillon, S. Boyle, J. Bridgland, S. Butland, L. Cabrera, R. Chapman, J. Chisholm, B. Chruszcz, D. Crossland, H. Dempsey, N. Denommee, T. Dobbie, C. Drake, J. Feltham, A. Forshner, K. Forster, S. Frey, L. Gardiner, P. Giroux, T. Golumbia, D. Guedo, N. Guujaaw, S. Hairsine, E. Hansen, C. Harpur, S. Hayes, J. Hofman, S. Irwin, B. Johnston, V. Kafa, N. Kang, P. Langan, P. Lawn, M. Mahy, D. Masse, D. Mazerolle, C. McCarthy, I. McDonald, J. McIntosh, C. McKillop, V. Minelga, C. Ouimet, S. Parker, N. Perry, J. Piccin, A. Promaine, P. Roy, M. Savoie, D. Sigouin, P. Sinkins, R. Sissons, C. Smith, R. Smith, H. Stewart, G. Sundbo, D. Tate, R. Tompson, E. Tremblay, Y. Troutet, K. Tulk, J. Van Wieren, C. Vance, G. Walker, D. Whitaker, C. White, R. Wissink, C. Wong, and Y. Zharikov. For our work near Canada’s ports in Vancouver, Toronto, Montreal, and Halifax, we thank R. Worcester, A. Chreston, M. Larrivee, and T. Zemlak, respectively. Many other organizations improved coverage in the reference library by providing access to specimens – they included the Canadian National Collection of Insects, Arachnids and Nematodes, Smithsonian Institution’s National Museum of Natural History, the Canadian Museum of Nature, the University of Guelph Insect Collection, the Royal British Columbia Museum, the Royal Ontario Museum, the Pacifc Forestry Centre, the Northern Forestry Centre, the Lyman Entomological Museum, the Churchill Northern Studies Centre, and rare Charitable Research Reserve. We also thank the many taxonomic specialists who identifed specimens, including A. Borkent, B. Brown, M. Buck, C. Carr, T. Ekrem, J. Fernandez Triana, C. Guppy, K. Heller, J. Huber, L. Jacobus, J. Kjaerandsen, J. Klimaszewski, D. Lafontaine, J-F. Landry, G. Martin, A. Nicolai, D. Porco, H. Proctor, D. Quicke, J. Savage, B. C. Schmidt, M. Sharkey, A. Smith, E. Stur, A. Tomas, J. Webb, N. Woodley, and X. Zhou. We also thank K. Kerr and T. Mason for facilitating collections at Toronto Zoo and D. Iles for servicing the trap at Wapusk National Park. This paper contributes to the University of Guelph’s Food from Thought research program supported by the Canada First Research Excellence Fund. The Barcode of Life Data System (BOLD; www.boldsystems.org)8 was used as the primary workbench for creating, storing, analyzing, and validating the specimen and sequence records and the associated data resources48. The BOLD platform has a private, password-protected workbench for the steps from specimen data entry to data validation (see details in Data Records), and a public data portal for the release of data in various formats. The latter is accessible through an API (http://www.boldsystems.org/index.php/resources/api?type=webservices) that can also be controlled through R75 with the package ‘bold’76.Peer reviewedPublisher PD

A Comprehensive DNA Barcode Library for the Looper Moths (Lepidoptera: Geometridae) of British Columbia, Canada

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.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.A catalog of these taxa meriting further taxonomic investigation is presented as well as the supplemental information needed to facilitate these investigations

A molecular-based identification resource for the arthropods of Finland

Publisher Copyright: © 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.Peer reviewe

The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life

DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life’s species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description. This article is part of the themed issue ‘From DNA barcodes to biomes’

Hymenoptera of 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

Forest biomonitoring, biosecurity and DNA barcoding

The economic, social and biological value of our forests makes their sustainability essential to our well-being. To ensure their long-term health, it is critical to regularly and effectively monitor their inhabitants, as well as to detect non-indigenous species early and accurately. These programs rely on the precise diagnosis of species, which can be complicated for terrestrial arthropods by sizeable trap samples, damaged specimens, immature life stages and incomplete taxonomy. The recent advent of DNA barcoding, a technique that differentiates species using sequence variation in a standard gene region, shows tremendous promise for circumventing these obstacles. This dissertation evaluates the integration of barcoding into forest arthropod biomonitoring and biosurveillance programs with several investigations of nocturnal moths (Lepidoptera) in British Columbia, Canada. Barcode reference libraries are constructed for looper moths (Geometridae) and Lymantria (Erebidae) tussock moths, and are determined to successfully discriminate species in over 93% and 97% of cases, respectively. The libraries demonstrate how barcoding might enhance biosurveillance programs by flagging two new records for geometrid moths, and by successfully diagnosing 32 intercepted tussock moth specimens. These two libraries, and a multi-gene phylogeny constructed for Geometridae, are used to conduct faunal inventories in modified forest systems, and investigate the influence of disturbance on three levels of moth diversity—species, genetic, and phylogenetic. A first level inventory of Stanley Park, Vancouver, produces a preliminary list of 190 species, the detection of four new exotic species, and the discovery of two potentially cryptic species. Surveys conducted across several harvest treatments at two silvicultural research forests display no evidence of increased diversity at intermediate disturbance levels, but do reveal a correlation between species and genetic diversity. And lastly, three levels of moth diversity are estimated in ponderosa pine systems that differ widely in attack by Dendroctonus bark beetles, and demonstrate a negative association between species diversity and tree mortality. In combination, all projects suggest that DNA barcoding provides several advantages over traditional biosurveillance and biomonitoring, including the ability to rapidly sort specimens, a reduction in specialist time, the detection of species at low density, and the ability to appraise multiple levels of diversity.Forestry, Faculty ofGraduat